The first time Michael is digging behind the sink, there are water connections to the back of it. Later in the episode, once Sucre has returned and Michael is removing the sink again, the water connections have disappeared.
When they show the flash back of Lincoln in his apartment after he left the parking garage with Terrence Steadman, you can see several tattoos on his arms but several times now through out the show they have shown his arms and he doesn't have the tattoos anymore.
When Scofield is talking to Sucre and unscrewing the bolt from the toilet, look closely at his fingers. He isn't actually unscrewing anything, there's no screw in the hole or in his hand, its all just well placed sound effects that make you think there is a screw.
Schofield is seen using a home made Allen key to remove a bolt from sink shroud. The bolt can already be seen to be missing and the sink is already loose from wall. Schofield then removes the tool and pretends to unscrew and remove the bolt by hand. It's clearly visible that there is no bolt yet he still makes the hand action. The sound for the bolt being removed has been added including the noise of it being dropped on the floor.
When trying to change Haywire as his cell mate, Michael is told that he is unable to warrant a change of cell mate without reasoning of physical or sexual abuse. In S1 Ep3, however, Sucre moves from cell 40 easily without reporting any abuse to him from Michael.