Revealing mistake: When Sara Tancredi is pulling her dead father off the door he lets out a very audible grunt and you can see his eyes and mouth moving around, a few seconds later he is on the floor and his eyes are dull and his skin slightly pasty. (00:16:40 - 00:17:05)
Revealing mistake: In the scene where Sarah crashes into the agent's buggy, you see they have been replaced with dummies. When the car first hits, you see one of the dummies fall out, but they are both seated in the next shot. Also you see that it is not Sarah driving but a man. (00:36:50)

Cute Poison - S1-E4
Revealing mistake: Near the end, when Michael is unscrewing the sink before kicking the wall in, watch his hands in the foreground while he is talking to Sucre. Just when Sucre says "But what you were doing up there in the infirmary." Michael starts using his fingers to take the bolt out. You can see that there is no bolt, just him turning air, with a mystery 'unscrewing' sound effect. (00:39:35)

Revealing mistake: When C-Note leaps out of the train, you can see that the man jumping out of the train is a stuntman. He is much chubbier than C-Note (wearing a life vest) and his face is completely different. (00:22:20)
Revealing mistake: When Pope bursts into the infirmary and sees Westmoreland's body, watch the collar of Westmoreland's jacket. You can see it moving up and down as though he's breathing. (00:03:30)
Revealing mistake: When Haywire jumps off the tower, it's obviously a stuntman falling down. And when you see his fall from above, he is falling towards a big drain. But when the scene cuts to the part when he has landed, he's lying on concrete. (00:42:15)
Revealing mistake: In the episode where Scofield, Sucre and T-Bag are driving in Panama, the trees in the background have no leaves - like Autumn/Winter in the US. And even though there of course are trees in Panama which shed their leaves, there is no time of year when all trees are leafless - like in the temperate zones. That shot was definitely not filmed in Panama.
Revealing mistake: When Sara crashes into the ATV to save Michael, you can see that the people on the ATV are switched out with crash-dummies.
Revealing mistake: In the final scene you can see Abruzzi in his cell where they have reused shots from series 1 in Fox River.
Revealing mistake: After Pope enters Scofield's cell to see the escape hole, we see him standing outside the cell looking out at everyone throwing toilet tissue etc. If you watch closely right after we see a guy pulling his pillows toward him to tear up, it cuts to another inmate who is throwing stuff out as well. Only thing is, we see the cell door slides to the side slightly which would indicate that the cell doors where not locked. In the event of an escape, lockdown would happen immediately, with all cell doors locked with the prisoners inside their cells. (00:04:00)
Under & Out - S3-E11
Revealing mistake: When Link is dabbing Sofia's burns its clear to see he's not actually making contact with her. Just making the motion. (00:26:10)
Revealing mistake: When 5 of the escapees are heading to Oswego to get the supplies and Michael tells Lincoln to turn right, you can see it isn't a real car as the steering wheel doesn't turn - Lincoln just moves his hand along the wheel. Watch the grooves and you will see. (00:18:50)

Revealing mistake: When Michael is thrown over the rails, it's a stunt double. (00:29:50)
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)

Revealing mistake: When Nika pulls up with the car at the end, there are tyre marks visible in the dirt from previous takes. (00:40:50)

Revealing mistake: When Linc drops the phone out of the car, it lands next to a very obvious blue marker. (00:21:30)

Revealing mistake: When Westmoreland knocks Bellick out, he misses Bellick's head with the thermos. (00:01:40)
Revealing mistake: When we see Nick's body with a gunshot to the head, you can see he's still breathing. (00:08:00)

And Then There Were 7 - S1-E11
Revealing mistake: When Nick is shot by Quinn, a blood pack is briefly visible under his shirt. (00:13:20)
Revealing mistake: When C-Note is hanging at the start, you can see he has some protection on under his jumpsuit as his build is a lot more stocky than his actual build. (00:01:30)
Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.