Goofs

The security guard with the tranq gun at El Bucho was one of the guards who died when the new Intersect blew up back in Season One.

Casey is providing air support for Sarah and Chuck during the day but when a car exploding is shown it appears to be at night.

When Chuck and Sarah are in the shootout toward the end, trapped on top of the building before they use a zip-line to escape, Sarah is shooting at the guys on the ground and her gun is clearly seen running out of ammo, with the slide locking back out of battery. However, three more shots are heard firing from her gun followed by her telling Chuck she's almost out of ammo.

When Chuck and Sarah are in the train station in Prague,a sign says "letenky" but in Czech, "letenky" means plane tickets.

Sarah tells Chuck to meet her at the 'Nadrazi Station'. In Czech the word 'nadrazi' means 'station'. However, the correct sign for 'Praha hlavni nadrazi' (Prague Main Station) can be seen on the platform.

During the shootout at the end, when Chuck and Sara get in the helicopter and Casey is shooting the mini-gun, you can see muzzle flashes from the gun yet it can clearly be seen that the barrel of the gun isn't spinning.

Sarah says Chuck shouldn't take the job as a spy because this would mean he can't ever be himself and constantly changing identities and hiding. Her solution is to just change his identify, hide and run away with her which has the exact same problem. Her solution doesn't really fix anything.