Deliberate mistake: Every time the commandos are seen in the early episodes of this season (The Freshman and Fear, Itself) they wear ski masks to protect their identities. Starting in The Initiative, they stop doing this. The reason is that the audience needs to be able to identify the different commando characters, but it's still a discontinuity.
Deliberate mistake: When Joey and Jonathan get in Joey's car at Metropolis (just before heading to the police station), the car has headrests. When they get to the police station, see Lance Gessler leaving and then follow him, the car no longer has headrests. Obviously removed so as not to obstruct the actors.