The drunken musicians passing the Riveras' house are singing "La Llorona," the same song Imelda sings.
Also, Miguel shines the shoes of a mariachi playing that song.
In the beginning of the movie, we're first introduced to Dante after Miguel passes a table full of Alebrije figurines.
In addition, near the far end of the table, is a model of Pepita, Mama Imelda's alebrije.
When climbing up to Miguel's hideout, Dante's footing displaces a few stacks of bricks, which would take quite a feat of strength to do effortlessly. This could hint that Dante is an alebrije and has supernatural strength because of it.
Also, in regards to "Dante's Lunch", there's the fact that Dante goes through an unusual amount of injuries whilst holding on to the bone (crashing clean through a fence, through tables of cacti, flour and luchador costumes). Normally, this would be taken as cartoon physics. But as it turns out, Dante is an alebrije, and it's likely he's much sturdier than the average dog.
When Miguel knocks over the photo and finds the hidden section, he asks Coco if this is her father, Ernesto De La Cruz. Coco never actually says yes - she points at the photo and says "Papa", but she never actually confirms that the name of the man in the photo is Ernesto.
In a bit of Freeze-Frame Bonus, the photo shows what Miguel thinks is Ernesto, but if you look at him, the man in the photo is noticeably less burly than Ernesto, hinting it's not him, and it turns out to be Héctor.
If you watch the video of Ernesto Miguel is watching near the start, the camera zooms in on his hands when he's playing notes, implying it's actually a stunt double. There are only wide shots of Ernesto when he's merely strumming, hinting he's actually not as talented as Miguel thinks he is.
Earlier in the movie, Abuelita asked Miguel "Do you want to end up like that man?! Forgotten? Left off your family's ofrenda?" It doesn't just foreshadow that Héctor (Miguel's real great-great-grandfather) is in reality nearly forgotten: it's a hint towards Ernesto's ultimate fate, forgotten and left off his "familia's"note the worldwide fans' ofrendas.
The fact that Dante can still see and hear Miguel after Miguel is transported to the other side despite no one else being able to do so likewise hints at the dog's true nature.
While sorting through the issue that Miguel is cursed, the Clerk explains that a curse is invoked when someone steals from the dead on Dia de los Muertos, on a day meant for giving to the dead. It's momentarily hand-waved why the guitar cursed Miguel when he 'asked' Ernesto for his permission to take said guitar, and there's even a Red Herring that perhaps it was Imelda's photo that might've been the "stolen" object. But it turns out, the guitar didn't belong to Ernesto, but rather Héctor, and Miguel unwittingly robbed it of its original owner.
Viewers who are familiar with Disney and Pixar villains being Shadow Archetypes of the heroes can readily identify the villain based on Miguels family admonishing him for following after his great-great-grandfather, combined with Miguel thinking the man in question is Ernesto de la Cruz.
When Miguel tells Dante that they need to find his great-great grandfather, Dante 'wanders off', immediately leading Miguel into the room where Héctor is being processed.
A subtle one in occurs when Héctor is being processed after trying, yet again, to sneak into the world of the living. The customs officer has a lamp on his desk whose colored, semi-translucent, lampshade casts an eerie green light onto a picture of Ernesto de la Cruz that's hanging on a wall.
Another one in the same scene, Héctor's Leitmotif during the entire scene is rusty guitar music.
Frida Kahlo immediately saw Dante for what he actually is, although she also quite humorously took it back later.
Upon meeting Héctor, when Miguel asks him how he knows Ernesto, Héctor says he used to play with Ernesto, and "taught him everything he knows". Since Héctor is introduced as a con artist, the audience takes this as a total lie. This turns out to be true. So true that Ernesto killed Héctor for his songs when Héctor was about to leave the life and go back to his family.
Also in the same scene, Héctor tries to play a chord, the same as Miguel had done at his shrine to Ernesto. He messes up, effectively throwing off the audience, but it's a notable Five-Second Foreshadowing.
Miguel's family angrily berates him every time he mentions his great-great grandfather, but not when he mentions De La Cruz. This is a clue that they're not actually the same.
At Frida Kahlo's studio, when Miguel is talking with Frida, Héctor enters the scene and scolds Miguel "not to wander off" or "bother the celebrity". At first, it seems like Héctor simply wants Miguel to remain low-key and stick with him. But a second time watching this, it's apparent Héctor is acting just like a parent would: making sure their kids learn not to wander anywhere without adult supervision, and not to bother strangers.
Speaking of Frida and Héctor, Frida is disdainful of de la Cruz hosting his party instead of rehearsing for the show the next morning, and so is Héctor. "That bum! Who doesn't show up to his own rehearsal?" Because Héctor, like Frida, is a true artist, and Ernesto de la Cruz is not!
When he's going on about Ernesto's talent at the beginning, Miguel says "He played in movies, he had a cool guitar, he could fly!" Ernesto does go flying at the end of the movie, thanks to Pepita.
Also in the above quote: Héctor can sing and he does have a cool guitar. But Miguel never considers whether or not Ernesto wrote his own songs. He never wrote a thing, every song he sung he stole from Héctor.
In the ripped up photo, the belt buckle of the mystery relative shows two crossed guitars, while Ernestos belt buckle is just normal with no guitars on it. The crossed guitars on the photo hints at a double act in the film, foreshadowing Ernesto and Héctors hardship and the fact Ernesto isnt who he seems to be.
Miguel tries to stagger to act like a skeleton, and Héctor tells him that isn't how they walk. Miguel points out that's how Héctor walks, which may be a clue towards Héctor approaching "Final Death" and gradually losing his energy.
When Miguel makes a big deal about how Ernesto de la Cruz is the best musician in the world, Héctor responds by acknowledging the songs Ernesto sings as pretty good while Ernesto's actual talent is only mediocre. Of course Héctor would know this: he wrote all of the songs that Ernesto claims are his, and no doubt recognized Ernesto for what he was — a medium talent who couldn't cut it.
Héctor takes Miguel to visit a forgotten friend of his to get a guitar and serves a couple of drinks, but the friend becomes Deader Than Dead and as such, Héctor drinks a single glass and leaves it upside down on the table, next to the full one. We learn later that Ernesto de la Cruz murdered him by slipping poison in a similar drink.
When Miguel excitedly exclaims that he's going to play "Remember Me" in the battle of the bands, Héctor immediately and uncomfortably negates the idea, saying that it's too popular and everyone will be singing it (which is true, and a legitimate concern). But later it's revealed that Héctor has a likely ulterior motive for not wanting Miguel to perform it: "Remember Me" is an extremely personal song to Héctor; he wrote it as a love song for his daughter Coco.
Dante's efforts to keep Miguel and Héctor together serves as foreshadowing for both Dante being a spirit guide and, again, Héctor being the real great-great grandfather.
During Miguel's Kick the Dog moment on Imelda, she sings part of the lyrics to "La Llorona" to convince him to listen to her reasons for banning music from the Rivera family. This foreshadows her performance of the song at Ernesto's Sunrise Spectacular.
When rescuing Miguel from the pool, Ernesto pushes his guitar out of the way before dragging him to the surface, showing he's trying to protect his reputation. In fact, we see later in the movie, namely when he's tossed into the cenote, that a guitar-deprived Miguel is a perfectly capable swimmer. The foreshadowing part of the scene is that no one tries to get the guitar back to the surface so Miguel may keep playing aka stealing the spotlight from Ernesto de la Cruz.
Ernesto is very surprised that he has a great-great-grandson. Since Miguel's great-great-grandfather had a family and knew his daughter, Ernesto shouldn't be this surprised he has descendants: the first clue that he and Miguel aren't related. He still goes with it, as it's possible that Miguel may be related to an unrecognized offspring... which given Ernesto's fame, might be a real possibility.
Similarly, when Miguel learns that Ernesto was his grandfather all along, his family incredulously responds "That's impossible." They know full well who his grandfather was, and it wasn't Ernesto.
Or they could mean "That's impossible, there's no way to instantly know for sure this stranger is the mystery great-great-grandfather." All the same, it foreshadows that it's impossible for a manlikeErnesto to be related to the family-orientated Riveras.
Ernesto tells Miguel, "I did all my own stunts." when watching one of his movies. In more ways then one, he did really do the stunt from that movie: poisoning Héctor exactly like the antagonist did.
When Ernesto learns that Miguel has to return home very soon or he'll die, he calmly states "Hm, I really should get you home" with the same casual indifference as if he just learned the kid was up later past his bedtime than he thought. He also tells Miguel that it's been fun and "I hope you die very soon." These are two subtle but tell-tale hints that Ernesto is a sociopath with no regard for human life, and willing to murder someone (like Héctor for his songs) when he thinks they might threaten his fame.
Doubling as Five-Second Foreshadowing; the marigold petal Ernesto uses for his blessing to Miguel does not light up like Imelda's when he starts the blessing, giving away the fact they're not related.
The headstock of Ernesto's guitar has a detail of a skull with a single yellow tooth. When Héctor first grins, it's hard not to notice that he, too, has a single yellow tooth, indicating that the guitar actually belongs to him; Ernesto de la Cruz has a mouth full of perfectly white teeth in both life and death.
In the flashback to the last time Héctor and Ernesto saw each other in life, Héctor is carrying a guitar case, which Ernesto picks up after Héctor dies, foreshadowing that the iconic guitar that led Miguel to believe Ernesto is his ancestor originally belonged to Héctor.
Mama Imelda wears a lot of purple, even having purple markings on her skull. Who else is the only other character noticeably wearing purple? Her husband and Miguel's true great-great grandfather, Héctor who wears a tattered purple shirt.
When Abuelita loads a bouquet of marigolds upon Miguel, he's still so upset about not being able to sign up for the talent show that he gets some petals into his mouth and spits them out. Héctor, too, is so upset about things not going his way that he ends up breathing flowers. Like great-great-grandfather, like great-great-grandson indeed.
Héctor uses shoe polish to disguise Miguel as a skeleton. However, he doesn't wear any shoes. Why would he carry around shoe polish, if not as a sort of keepsake to connect him to his shoemaker family?
When Miguel asks Ernesto if he regrets leaving his family behind, Ernesto vaguely talks about it being difficult but couldn't resist his calling - notice that he never mentions any specific people, he doesn't use Imelda or Coco's names or even bring up a wife and daughter at all, because of course, he's not Miguel's great-great grandfather and what he meant by family was probably his parents or his hometown.
If examined closely, Héctors bangs are straight parted and messy like Miguels, while Ernestos are curled and slicked back. Héctor also shares Miguels Beauty Mark and dimple when alive, while Ernesto doesnt. This is a hint of Strong Family Resemblance indicating who the real great-great grandfather is. Which makes even more sense when Miguel himself is the one that draws attention to the fact he has a dimple on one side when he smiles but not the other!
Chicharron says right before dying that the song Héctor played for him "brings back memories." By the end of the movie, it's a song that helps Coco renew her memories of her father.
Very noticeably, not once does Miguel's family in the land of the dead ever refer to his great-great-grandfather by name. Of course, had anyone even said Héctor's name around him or had Miguel mention Ernesto de la Cruz around them, the plot would have gone differently. He also never brings up their names around anyone else, not even Ernesto, who only vaguely knew Imelda as she was his best friend's wife.
The musicians making fun of how Héctor died (by allegedly choking on some chorizo), and Héctor defending his position by saying it was from food poisoning. Taken a step further by Héctor complaining afterwards about musicians being a "bunch of self-important jerks!"
Only after seeing the "seize your moment" motto printed on de la Cruz's statue does Miguel perform questionable acts to get into the talent show (stealing an offering from another ofrenda to distract Dante, breaking into Ernesto's tomb, and stealing his guitar). Ernesto did some pretty shady things himself to seize his moment, such as killing his friend Héctor and taking the credit for all his songs.
Héctor admits that eventually, everybody ends up forgotten by those in the land of the living, exactly what starts happening to Ernesto once the truth is revealed.
The poster pretty much sums up everyone's role in the film. The guitar played by Ernesto de la Cruz divides the Land of the Living and the Land of the Dead. Ernesto is positioned between Héctor and Imelda, hinting that he's the reason they are separated. Two skeletal hands are touching the guitar; one is undoubtedly Héctor's, while the other could be either Héctor's or Ernesto's, foreshadowing Miguel's mistaken belief of the identity of the guitar's true owner. Imelda being at the bottom of the poster foreshadows the weight of the years that passed since her husband's departure, as well as her caring attitude in spite of it. Miguel and Héctor being at the top foreshadows that they are family. Dante being across from de la Cruz foreshadows him as an alebrije, protecting Miguel from harm. And Coco being at the bottom foreshadows the struggles she herself endured in wanting to see her father again.
In the deleted scene "Tour Guide", Héctor (as a tour guide) mentions that part of his "craft" is showing tourists "there's more to this city than de la Cruz; there's art, culture, history". Meanwhile, the bus drives by a bunch of de la Cruz posters. It may seem Played for Laughs, but it's meant to represent the Irony that despite being lauded as a great artist by the world, de la Cruz does not represent art or culture as much as he does fame and attention.
He also makes a frustrated fuss about Miguel interrupting his "craft", like any artist would at having their art disrupted.
According to Héctor, the reason he no longer makes tours near Ernesto's house is because Ernesto asked him a favor to stop driving by his house. It becomes very obvious foreshadowing that Ernesto wants Héctor as far away from him as possible, either so he won't suspect he earned his fame with Héctor's song, or because most murderers want to stay away from their victims.
Another deleted scene "Alebrije Attack" has Miguel and Héctor eating tangerines on their way to Plaza de la Cruz. Just like the ones Miguel shared with Mama Coco in the beginning of the movie.
In the deleted scene "Bus Escape", Héctor says that when you're faced with loneliness that separates you from loved ones, the only thing that can save you is a song. One can only guess how a song saves him in the end.
The deleted scene of the showtune "prologue" starts out with a reverent and beautiful ballad, before it erupts into an over-the-top show tune that practically bastardizes the very meaning of Dia de los Muertos. Dia de los Muertos is meant to be a personal holiday, meant to reverently pray and visit dead family members. This could've been intended to foreshadow how Ernesto took something as personal as "Remember me", and twisted into something flashy and showy to garner attention.
There's a blink-and-you'll-miss-it moment, right after Ernesto takes the now-dead Héctor's songbook and flips through it, where "Remember Me" (and "The World Es Mi Familia") is shown. The song notes above the notation state "simply, tenderly," as lullabies are sung. This sets up for when Héctor sings it as it should have been performed (instead of the bombastic, over the top ballad Ernesto turned it into). Doubles as well to point out subtly that Ernesto may have taken Héctor's songs, but he didn't have the talent or skill to ever perform any of them how they should have been done—and it's likely that none of the songs were ever sang properly by Ernesto the way Héctor intended for them.
The photo features the great-great-grandfather's head missing as it was torn off. The photo Héctor gives Miguel is only his head. A subtle nod that it's his head that was missing from the picture.
Both Imelda and Héctor react very similarly to tech (if less violently in Héctor's case) with Imelda calling a computer "devil box" and Héctor calling the scanner a "blinky thingy".
When Héctor sings to Chicharon, he changes a lyric to be more kid-appropriate in the presence of Miguel. It's a hint that Héctor is a parent himself.
When Héctor confronts Ernesto while the latter was about to give a blessing to Miguel, watch closely. Ernesto is pushing Miguel in front of him, not behind him. And this is when Ernesto didn't recognize Héctor and thought he was a potentially dangerous stranger. In other words, Ernesto was going to use his supposed great-great grandson as a shield. A subtle hint that Ernesto isn't a good guy.