-He was probably already in the library, didn't break in only after cop left. Probably broke in while the station was closed previously.
-St Cloud police literally have probably never seen an attempt like that, still don't know what was in the syringe, and yeah sometimes electronics do temporarily have issues. It's not weird for them to be confused by a potential elaborate conspiracy.
-Emmit had to leave the scene of the crime immediately to establish an alumni.
-Emmit was over eager in trying to establish that alibi, was clearly somewhat drunk, and likely in a state of shock from just killing his brother.
-Varga knows that Nikki can point a finger at his goons so it's better to just kill her to minimize any possibility of blowback. He also knows that she can point to a feud between emmit and Ray about the stamp, so it would basically make Ray a viable suspect if that whole plot is discovered, which obviously Vargas doesn't want.
The most unrealistic thing is that the prison bus did not have a police cat escort in case something happened to the bus. That oversight was worth it though imo for the action and surprise of the scene, and intrigue if Nikki can get out of it. Imo at least.
Basically nothing you said is actually contrived though. If you don't think cops tend to just stick with a suspect even if there is compelling evidence of another suspect I don't know what to tell you. It's how people get wrongfully convicted all the time.
