Many fans were not surprised to find out that Gall Trayvis was really an Imperial agent.
A couple people figured out that the stolen TIE fighter from "Fighter Flight" wasn't actually destroyed (judging from information in the episode's trivia gallery), and that it would serve as a Chekhov's Gun.
Fulcrum is Ahsoka Tano. People actually figured this out from "Fulcrum"'s debut episode!
In "Call to Action" Kanan tells Ezra "I'll be right behind you" to encourage him to run while he holds off the Imperials. Most people guessed that it was something his master said to him during her Heroic Sacrifice, which was proven correct in the second issue of Kanan.
People figured out that the Seventh Sister was a Mirialan based on her appearance in a bit of concept art that showed her green skin. Unlike most examples, however, it was part of a larger fan-speculation that did not come to pass, as most were betting on her being Barriss Offee, a fallen Mirialan Jedi and former friend of Ahsoka whose last known fate was being imprisoned under Republic custody in Star Wars: The Clone Wars. After "The Future of the Force" aired, the possibility of that falls close to none as the Seventh Sister was completely out of her league against Ahsokanote Whereas Barriss was able to beat her in combat through skill and trickery. and neither acknowledge any recognition beyond hunter and hunted. Star Wars: Tales of the Empire would be the series to elaborate on Barriss' actual fate, which reveals that she has indeed become an Inquisitor.
A single piece of info from All There in the Manual said that Sabine inherited her Nite Owl helmet, leading to support the theory that Sabine's mother or another female relative was ex-Death Watch. Also somewhat supported by her neutral comments on Death Watch in her journal. Come "The Protector of Concord Dawn", Sabine reveals her mother used to be Death Watch.
Some people suspected that Kallus was lying about giving the order to deploy disruptors on Lasan, due to the Fridge Logic of having an espionage agent making a big decision that should belong to a more superior power such as a general, as well as a a mysterious lack of information from his POV in the "Droids in Distress" novelization (as in, it never says anything like "He remembers how he gave out the deployment of disruptors", and instead says things like "The Lasat should've died a long time ago, and it was time to fix that fact."). It gets proven true in "The Honorable Ones", where he admits that it wasn't supposed to be a massacre, suggesting that he was ordered by someone else to use the disruptors.
When Word of God revealed that the Grand Inquisitor had shown up in The Clone Wars, one theory was that he was a former guardian of the Jedi Temple, since they always kept their faces covered and wielded double bladed lightsabers. Come "Shroud of Darkness" and one of the Temple Guards in Kanan's vision reveals himself as the Grand Inquisitor. Later on, Dave Filoni confirmed that he was indeed once a Temple Guard, specifically one of the guards who arrested first Ahsoka and then Barriss Offee, and was filled with doubt after Barriss' proclamation that the Jedi had been corrupted.
Another common theory was that the Dark Side planet seen in the final Season 2 trailer was Malachor (based on the planet's general appearance, and being alluded to in supplementary material for The Force Awakens as the place where the design of the crossguard lightsaber originated). Come "Shroud of Darkness", it's made clear that Malachor is this very destination.
The Fifth Brother's Animal Eyes looking similar to cataracts and the show's emphasis on his skill with the Force (especially sensing others) caused people to believe he was blind. An interview with his voice actor revealed that his work-in-progress name besides the "Male Inquisitor" was, in fact, the "Blind Inquisitor".
Quite a few people guessed that Ezra's new lightsaber would be green before it was confirmed. Supported by when Filoni tweeted a photo with an angled green laser behind Rex back on May the Fourth, prior to Celebration 2016.
When Filoni tweeted another photo of an unknown dark green object with jaig eyes, one of the guesses was that it was Kanan's mask. This ended up being the case.
Shortly after being cancelled, Disney Infinity revealed on its YouTube channel that Hera (whose figure had been conspicuously missing from the crew line-up) would've been released later on in 3.0's life. Some noticed that Hera had a different torso from her current appearance in the show (around the time Season 2 ended), leading to guesses that this was her Season 3 appearance. This ended up being correct, and this also suggests that her figure would have been released towards the end of 2016.
Long before the release of the third season trailer, articles had discussed rumors of Thrawn's immigration to the EU canon on Rebels.
People felt like Sabine would get a jetpack, considering it would be jarring if she was the only Mandalorian warrior without one. Gets lampshaded towards the end of Season 2, before it turns out she gets a jetpack in Season 3.
Considering everything she had been through and The Reveal that she was of House Vizsla, it was guessed that Sabine would be the next holder of the Darksaber at some point, and this would have something to do with Maul/the Mandalorian Myth Arc due to its fate being undisclosed. Come Season 3, and she is the new owner of the Darksaber, with Word of God saying that it will end up being a plot point for Sabine and the Mandalorians.
People immediately called the new Fulcrum being Agent Kallus who has committed a Heel–Face Turn once a new Fulcrum was revealed and Kallus was suspiciously absent in the Season 3 trailer. Building up to The Reveal in "An Inside Man", people not only found Fulcrum's voice familiar, but Kallus' behavior also raised some eyebrows (such as helping the pilots defect and showing discomfort with Thrawn's modus operandi).
Many had speculated that one of Maul's goals following his escape from Malachor would be to seek out (and kill) Obi-Wan Kenobi. In "The Holocrons of Fate", this is heavily implied to be the case, and it's outright confirmed in "Visions and Voices".
For Rogue One, through Epileptic Trees, people assumed that Chopper was sent over to England to be cast in the film rather than for Celebration (where he was absent). He makes a cameo appearance in the background.
Also, ever since Rogue One was announced, people also guessed that the Ghost would get a cameo appearance as a Freeze-Frame Bonus in the Rebel fleet, and that the most likely member to be at least mentioned being present would be Hera. With Chopper being present, a "General Syndulla" being mentioned (confirmed to be Hera), and an unnamed VCX-100 (also later confirmed to be the Ghost) among the fleet, they got it on the money.
Some assumed that there were more Fulcrums or rebel informants with codenames than just Ahsoka, which was confirmed in Season 3. People also then came to guess that Cassian Andor from Rogue One was a Fulcrum, due to being a recruiter and a member of Alliance Intelligence, which would then be confirmed in All There in the Manual.
It was guessed that the Imperial supercommando accompanying Sabine's clan was Sabine's older brother, once it was revealed that Sabine has a living brother.
For non-Rook Kast theorists, some of them guessed that Sabine's last name was actually inherited from her mother.
When Sabine got a hold of the Darksaber and began her training in "Trials of the Darksaber", some complained that she had no claim and leadership over it because she did not formally kill Maul, the last holder of the weapon, in order to receive it and instead looted it from his stuff. This was actually addressed in the next episode, "Legacy of Mandalore", where another character points out this exact problem, with the new holder pointing out that this is as good as it gets (because Maul has no interest in Mandalorian affairs anymore and there is no way she'll be able to defeat him), affirming later that she doesn't intend to becoming a permanent leader of Mandalore and instead wants to reform Mandalorian culture so that it can be more universally beneficial.
People guessed that due to a lack of mention in post-Rebels works, the Mandalorians either stay independent from the Rebellion, have a minor role in the Rebellion, or a Mandalorian uprising fails, with the first two possibilities being what happened with the Free Ryloth Movement earlier on in the show and as we learn later in Bloodline. In the ending of "Legacy of Mandalore", a character says that the Mandalorian Resistance will rise on its own, independent from the main Rebellion, at least for now.
Starting all the way back from pre-release information that Kallus is an Imperial Security Bureau officer, many immediately guessed that Yularen (who is involved in the Imperial agencies) would make an appearance in regards to Kallus's job. A connection between the two was confirmed in All There in the Manual before Yularen himself debuted in "Through Imperial Eyes". It was also correctly assumed that Yularen had a good memory of Kallus and that Kallus looked up to Yularen, but it was debunked that the two interacted on a regular basis and a bit beyond just a superior-subordinate relationship, as the episode revealed that Yularen only remembers Kallus as a star pupil at the Royal Academy and that Kallus does indeed idolize Yularen. However, it did also confirm that Yularen would be disappointed in Kallus for being Fulcrum.
When Lyste was shown to be involved in "Through Imperial Eyes" as being alongside Kallus, it was guessed that Kallus was going to frame Lyste as being Fulcrum.
The masked bounty hunter from the second Season 3 trailer being a disguised Ezra sent to help retrieve Kallus in that episode as well, people being tipped off by Sabine's stylized design of a lothcat on his helmet and the same boots that Ezra has. Funnily enough, even though Thrawn never got to see Ezra in this disguise in the episode, he also deduced in-universe that it was Ezra by the art on the helmet.
Obi-Wan's line from the Season 3 midseason trailer, "You're in the wrong place", actually being directed to Ezra as a part of their meeting and not a Pre-Asskicking One-Liner to Maul.
The Cavalry in the summaries for "ZeroHour" was guessed to be either the Bendu and/or Clan Wren. It is indeed both.
Sato and Konstantine dying by the end of Season 3, likely having something to do with each other in regards to Thrawn.
Kallus surviving Season 3 to join the Rebellion.
A minor one, but fan artists were fond of messing up Kallus' hair (with pseudo-bangs), often in the context of being in a fight. He gets beat up in "Zero Hour" by Thrawn, and his hair gets tussled similarly to how fan artists depicted.
There was actually an instance on Tumblr where a couple of users were trying to figure out the musical cues of the characters, with someone guessing that the cue in "Art Attack" after Sabine escapes her explosion was her cue. Cut to about year later, and they were right.
Rau and Bo-Katan having met in the past since the former is essentially the leader of the Mandalorian royal guard while Bo-Katan is a Fallen Princess, as well as that the two were active during the Clone Wars. While it isn't explicitly confirmed, the two have moments that imply they've worked together before in the past. It was also guessed that the two's personalities would be Red Oni, Blue Oni until it becomes a fire-forged friendship/Back-to-Back Badasses, which is only implied or briefly shown.
Kanan dying in the second half of Season 4 (which, had been theorized for every season in the show, so it had to be true at some point), which is related to...
Kanan is the wolf in the Season 4B trailer, due to sharing a similar facial structure (including blue eyes) and being friendly to Ezra.
The fate of Ezra and Thrawn at the end of the show being that they went MIA and are somewhere else in the Galaxy.
Sabine being involved in Ezra's fate at the end of the show.
Given the events of "A World Between Worlds", Ahsoka showing up at the end of the finale to look for Ezra.
Hera being pregnant with Kanan's child at some point during the show, with the epilogue showing that she's taking care of their baby.
Thrawn's fate having to do with literal tentacles, as the Bendu prophesied at the end of "Zero Hour" that his defeat involved him being "surrounded by many arms in a cold embrace."
that Hera (whose figure had been conspicuously missing from the crew line-up) would've been released later on in 3.0's life. Some noticed that Hera had a different torso from her current appearance in the show (around the time Season 2 ended), leading to guesses that this was her Season 3 appearance. This ended up being correct, and this also suggests that her figure would have been released towards the end of 2016.