- In the flashback at the beginning of "Best Fronds", Sasha and Marcy are hit by the same light coming out of the music box that transports Anne to Amphibia. The end of the episode reveals that the two of them were also transported to Amphibia, albeit in different parts of the dimension.
- In the first season episode "Stakeout", when Anne is tripping on Hop-Pop's energy drink, she hallucinates that she has glowing blue hair and shoots laser beams. Anne gains those powers for real by the end of the second season.
- After winning the election in "Hop-Popular", Mayor Toadstool tells Hop-Pop that a frog beating a toad "would've made headlines". "Reunion" reveals that just the act of running against Toadstool was enough for Hop-Pop to make headlines.
- In "Wally and Anne", Anne tells Wally how in her world reputation means everything, which is why she's so concerned about proving the Moss Man exists. Wally points out that since Anne has been transported to Amphibia she has the perfect opportunity to reinvent herself and be a whole new person. Turns out Sasha and especially Marcy took the opportunity the reinvent themselves to an extreme.
- In "Cursed", the newspaper Anne briefly hides behind has the headline "Rebellion gains steam". In "Reunion", it is revealed that Hop-Pop challenging Toadstool has led to frogs all over the valley being inspired to rebel against the toads.
- On the official poster for S2, King Andrias is far in the back and darkly shadowed. He also appears to look sinisterly at Anne with interest. This hints that there's something dark and dangerous about him.
- When Anne draws the sword she got from Tritonio Espada in "Combat Camp", as well during as her duel with Sasha in the season 2 opening, the blade glows blue. This both foreshadows her connection to the blue gem and the sword's connection to the Calamity Box, as an illustration of it is shown alongside a bow and dagger in King Andrias' book in "A Day at the Aquarium".
- There's a very subtle hint toward Marcy becoming a host for the Core, in which Marcy's picture in the Crowded-Cast Shot at the end of the S3 theme is replaced with Domino in the final product.
- When the girls find each of the three temples necessary to recharge the gems, the setup of said temples is designed solely around recharging the gem alone, and none of the carved murals in the temples showcase the music box or explain how it ties into the gem's intended usage. When Marcy inputs the necessary combination to release the gems from the box, they're shown to be held as part of the box by mechanical grips, akin to the Magitek machinery that Newtopia once ran on. This hints at the reveal that the music box itself is an artificial addition to the gems, designed to weaponise them from their true intended purpose and power both Newtopian society and interdimensional travel, since using music notes as coordinates is how one opens portals between different worlds.
- When Marcy is freed from her healing chamber, she is wearing a mech suit with an ominous eye jewel on the chest, in the same design as the eyes of the Core. Also, the amphibian text on the chamber translates to "Host". Both foreshadow Marcy being chosen as the Core's human host.
http://tvtropes.org/pmwiki/pmwiki.php/Foreshadowing/Amphibia
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