Other mistake: When Michael climbs up the rope to get to the room below the infirmary, the rope is hanging from the manhole cover, but he still manages to lift the cover whilst hanging from it. In the next shot where he looks down the manhole, its clear that there is nothing other than the rope he could have held on to while lifting the cover. An impressive accomplishment, defying the laws of gravity. (00:38:00)
Suggested correction: I disagree, in the earlier episode where Michael actually climbs out of the water and attaches the rope, when climbing up through the manhole cover he uses a lip to support himself first.
Yes but the point of the mistake is that Michael is solely hanging from a rope that is attached to the man hole cover. While his weight is on the rope, he managed to lift the manhole cover. The lip mentioned is created when the cover is lifted.
The water at the correct level helps him to swim up and push the metal attached to the rope.

Continuity mistake: When Kellerman orders Hale to give him his weapon, Kellerman pulls out his own weapon with his left hand. In the next shot, his gun is in his right hand, and he then transfers it back to his left. (00:36:45)
Revealing mistake: Michael climbs out of the hole during the escape in his coveralls. When he looks down to shout to the others to say it's clear he has no top on. The shot is reused from when he first climbed up. (00:37:10)

Visible crew/equipment: As the helicopter takes off at the start, the filming equipment is reflected. (00:02:00)