These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ass Pull: It's hard to imagine the returns of Sara and Kellerman after they were both presumed dead were well thought out in advance. Also is that the fourth season opening shows us that the Sona prisoners escaped; C-Note's happy ending in season 2 is ignored; the company's very public reveal in season 2 has been ignored; Lincoln is revealed to have been a killer in his backstory - when it was repeatedly established that his character was incapable of doing so; Kellerman comes up with a contrived way to resolve everything at the end of the series with no foreshadowing; Michael and Lincoln not actually being biologically related, the list goes on.
Canonical, if unidirectional. T-Bag has had "designs" on Michael since their first meeting. It's not subtle. His nickname for Michael is 'Pretty'.
Gretchen and Sofia. Gretchen continuously comments on how pretty Sofia is and seems to have No Sense of Personal Space with her. Also, there is Gretchen and Sara.
And Gretchen and Linc is canonical, if also one-sided. There are two points when Gretchen wants to have sex with Linc and tells him so.
God-Mode Sue: Michael Scofield. No plan will work without his involvement. He starts to become entirely precognizant in season 4.
Harsher in Hindsight: Tweener's actor Lane Garrison went to prison for real after killing a girl while drunk driving shortly after finishing filming his role on the show (the timing was so tight that he was still appearing on the show for a couple months after going behind bars).
Ho Yay: T-Bag and everyone, especially Michael, but it's completely one-sided on his part.