We learn in a later episode that the Sunakies/Snackyes have bodies made of sand, and only sand. In one of the last episodes, Erika, Itsuki, Coffret and Potpourri dress up like Sunakies/Snackyes to sneak inside the villain's base. Think for a minute... what happened to the poor Sunakies/Snackyes whose clothes they got?!
Another from the last episodes involving Yuri. She reunites with her long lost father just in time for him to die before her eyes. Assuming she doesn't tell her mother that she's Cure Moonlight, it can be assumed that she also doesn't tell her mother what happened to her father. She'll spend the rest of her life living with this secret, while her mother spends the rest of her life wondering when/if her husband will come home.
It can be softened into thinking that Yuri necessarily lied to her mother that she heard news that her father died in an accident. It would bring sadness, but it could happen before the epilogue scenes and implies that they eventually got over it. Typical hero identity coverage.
In episode 7, when Tsubomi panicked as Erika was suggesting for her to pine on someone other than Itsuki, the other watching students were looking at her and in Tsubomi's mind, they probably was thinking "Be quiet, training is in session"... but they didn't glare at Tsubomi's second yell about finding her first love. On closer look, their faces aren't even annoyed with the loudness and in fact look amused. When Itsuki's Unsettling Gender Reveal hits in... it hits to this troper that the message these students are conveying is instead "Poor girl, she doesn't know the horrid truth about Itsuki's gender..." in an amused way. Fridge Moment of Funny?
In episode 9, near the end, a little girl approaches Hanasaki Flower Shop asking for sunflowers, and Tsubomi tells her it's not sunflower season yet ("Sunflowers love the summer, when the sun is at its brightest!"). Now, remember that Cure Sunshine's first episodes came right before the beginning of the summer vacation arc that is a staple in the franchise. What is Cure Sunshine's signature flower again?
Dark Pretty Cure is pretty explicitly an evil counterpart to Cure Moonlight- however, the rest of the pretty cure have evil counterparts as well, hinted at by their respective coloration or role.
Sasorina mirrors Itsuki's dedication, and shows what Itsuki might have become if she let her dedication to her brother get the best of her- someone who gets too many second chances and ends up getting in too much trouble and feeling unfulfilled.
Kumojacky represents Tsubomi's pursuit of strength and extroversion. Though Kumojacky is indeed strong, he is somewhat cowardly and he lacks the gumption to protect himself or his coworkers.
Cobraja represents Erika's jealousy of her sister in his pursuit of beauty, which ends up being his undoing when he allows himself to be purified.
Finally, Sabakku is similar to Kaoruko, being an older mentor to the others as well as the ancestor to one. But while Kaoruko teaches the others by being honest about her shortcomings and mistakes, Sabakku's mistakes end up being his undoing.