So toward the end it is mentioned that people used various parts of Junko's body for various reasons, like one person transplanting Junko's eye into their head or Komaeda attaching her hand to his own arm. But that shouldn't be possible at all. If her body was flattened during the Detention part of the execution, how was any part of her that salvageable?
It's possible they were too caught up in their obsession to CARE whether the parts were actually salvagable or not. Komaeda mentions he can't actually MOVE his left hand...
I would think that the reason he couldn't move it was because the surgery to attach it wasn't done properly. Most likely, he actually cut off his own hand and just stitched hers onto the stump. Going by how crazy the Despair students are said to be, it wouldn't be surprising if they took her body parts and mutilated themselves to attach them without any medical help, because that just gives them more despair and shows how far off the rocker they are. And even if that's not the case, it still doesn't explain how there were parts of Junko still around when her body should have been pulverized to a pulp- literally. The Detention execution didn't dismember her, it squashed her! And going by how big the block was and how she was positioned, there should be nothing left of her that isn't flattened, let alone perfectly intact like her hand or eye. Of course, this is Dangan Ronpa so there probably is no reasonable explanation for how or why.
It's probably Mukuro's.
Even in that case, while her hand was salvageable, her eye probably was not. Of course, that might make it even MORE despair inducing.
Gundam's execution isn't an ironic death at all — it's exactly the kind of romantic death they claim they want just before going to the execution. Why did Monobear choose to do that instead of twisting the knife at the last moment like he usually does?
It's ironic because he's trampled by animals. On top of that, the magical circle he draws to protect himself does a grand total of jack shit — much like how all his posturing and grand declarations amounted to nothing. And the being lifted off to heaven by angel animals, assuming Monobear's responsible for staging that part, mocks the Dark Overlord image he's built around himself.
Monobear didn't seem to have control over the magic circle. That's ironic from a literary perspective, but not from an in-universe one. And while being carried off to Heaven may have subverted the dark overlord thing, the "lifted up to the skies to be immortalized in the stars" is the kind of thing he seemed to want in his pre-execution spiel. The whole thing is just very romantic and fantastical in tone, but seems absent of mockery like, say, Celes' was. Maybe the irony is supposed to be subtler than normal and I'm just not seeing it, I don't know.
No, he didn't. Gundam did. That's part of the irony — Gundam's using the powers he bragged so much about to try and protect himself... and they fail. Not because Monobear interfered with them at all — they just flat didn't work.
In the second trial, why does Peko do that spiel about how the students should let her go free because she's Kirakira and needs to do justice etc. if she wanted to get pinned as the culprit? If the students did as she asked, they most likely would have voted for Kuzuryuu instead (since he was the most suspicious next to her), which would have utterly ruined her plan.
That's all about staying in-character and convincing them she's really Kirakira. She doesn't really expect them to listen to her; she's just playing her role to the hilt. Making it look good.
In chapter 2, why did Peko choose such an absurd story for her alibi? People in the Let's Play thread were speculating that it couldn't possibly be her, because who in the world would make their alibi for murder "I went looking for the other islands and they just weren't there"? It's too unbelievable — it would place her under suspicion immediately. Why didn't she just say she went for a swim instead of also making up a story about nonexistent islands?
Because she wants to be caught. Getting the others to suspect and finger her for the murder is all part of her larger gambit to save Kuzuryuu. But offering no alibi whatsoever would look too suspicious, so instead she gives one that the others might accept on its face... until Fridge Logic kicks in and they look at it a little harder.
In the final trial, when Makoto, Kyouko and Byakuya enter the virtual reality, shouldn't their memories of being in the virtual reality have been erased when the forced shutdown commenced? They say so themselves that in the event of a forced shutdown, any memories they obtain within the virtual reality will be erased when they are brought back to the real world.
Perhaps this is proof that this wasn't true after all - for them or for the others.
Why didn't Komaeda realize that Nanami was the traitor sooner? Being a self-proclaimed SHSL fanboy, he has admitted to looking up information regarding his classmates before coming to the school. And indeed - he provides some extra information about each student in the prologue as they do their introductions. All except for two - Hinata and Nanami. The former because Hinata was never a proper Hope's Peak student, the latter because she doesn't even exist in the real world. In fact, Nanami herself seemed surprised when the file containing all their profiles included hers - suggesting that she wasn't actually based on an existing SHSL student and that her 'profile' was just a dummy made by Monokuma. Therefore, Komaeda wouldn't have been able to find any information on her - which should've been immediately suspicious when he's considering possible candidates for the traitor.