When Sucre is building the bridge to the glass wall to steal Scylla, just before the canister of liquid nitrogen falls, it changes from lying straight across the wooden panels to a almost 90 degree angle and then back to straight, before it falls.
In the scene where Sara is sitting on the bench, we see the reflection of the camera crew in her glasses.
When breaking through the wall the metal barring entry is clearly seen. Next scene the bars are gone, allowing entry. Removing the bars would be a loud action that would set off the alarm. No explanation was given as to how they were removed.
When clearing the safe house, both Agent Self and Agent Holtz handle their firearms improperly, despite being trained FBI agents. Specifically, Self has his entire index finger wrapped around the trigger, and Holtz holds her weapon with the incorrect "teacup" grip (palm under magwell). Both are fundamental mistakes that a trained FBI agent would never make.