One of the most misunderstood episodes in the 2012 version has to be the Fear Mushroom episode.
April is shown to be afraid of bats. But really it's to show how much she's afraid of losing her dad to his mutation.
Casey is shown to be afraid of rats. This is pretty common with people, however, I believe this fear stems from that episode when The Rat King is first introduced and rats overtook the city.
Mikey is shown to be afraid of the Squirrelinoids. However, this shows us that Mikey's really afraid of reality. The squirrelinoids were that of fantasy from a simple comic that became real. It showed us that Mikey had realised that his world was becoming more and more dangerous. That the real monsters were those found in the real world. That reality is scarier than fantasy.
Donnie is shown to be afraid that April would hate him. While Donnie's crush on April had a small influence in that, what he's really afraid of is being rejected by those he cares about. April was Donne's first ever HUMAN friend, someone who looked at him as an equal. This only hammers down more when we hear the lines "I hate you, you mutated my father." Donnie still blames himself for nearly losing his best friend. That's also why Donnie was so desperate to get April back. It wasn't just because he had a crush on her, but because she's the only connection he has to being normal.
Raph is shown to have his common known fear of cockroaches (which is later to be found out that he is afraid of all bugs). However, I believe this is a metaphor for his true fear. While it was expected that his fear would be him losing his temper, Raph knows that he and his brothers won't let him get that far. Cockroaches? An insect that can survive a nuclear war? That's not something Raph can control. And while he DOES have a phobia of insects, Raph is most afraid of not being able to control his environment or the situation surrounding him.
Leo is shown to be afraid of letting his team down. While this is true, he has expressed that numerous times, it branches out to being afraid of failure. Leo doesn't just fear he'll fail his team, he's afraid of failing his brothers in a way that could potentially lose their trust or, worse, kill them.
hits every single point and does NOT miss omg