In "Crazy For You," when Shawna Baez was placed in the pipeline, it was stated that her cell's window was a one-way mirror to prevent her from teleporting out of the cell; however, when she is returned to her cell, the inside of the glass is just a normal window.
When Firestorm and Flash hit the ground after Flash catches him, Firestorm's eyes are normal instead of the glowing white of his powered up state.
There is no laser-eyed Meta-human in season one of The Flash, but in Rogue Air when they transport the Meta-humans there is one. This is due to him staring in The Arrow that is set in the same universe as The Flash.
When fighting The Reverse Flash, The Arrow shoots him with an injection arrow containing nanites that emit a high frequency pulse to disable the Reverse Flash's speed. The Reverse Flash counters this by vibrating his body at super speed to separate himself from the nanites - but how can he use super speed to remove nanites, the sole function of which is to prevent him from using super speed in the first place? Did they stop working? If so, then why did he bother wasting time separating himself from them in the first place? It could be that they severely inhibited his speed but did not completely disable it, allowing him to perform smaller feats such as this. No explanation leaves it a plot-hole (especially since the second nanite arrow works completely).
Incarcerating meta-humans in the Partical Accelerator has always been a terribly inhumane punishment within an impossible imprisonment. Impossible? Yes. If Mist, who can turn into a gaseous state, can't get out, neither can food, water, nor fresh air get in, sentencing those within to starve, desiccate and suffocate. Inhumane? Yes. Humans need input. (Babies deprived of it suffer permanently deformed personalities.) Those at S.T.A.R. Labs have created a hell-hole like no other, where captives face life in perpetual solitary confinement, unable to talk with anyone (unless by rare visit of a jailer), and with no chance at rehabilitation or redemption (which for Peekaboo, a non-hardened criminal and the best candidate for eventual release, is a crime). Plain and simple, they ARE left to rot. Their developed outrage at being thus confined by "the good guys" is justified. Their escape - more of a positive outcome than it should be.