Plot hole: After the nuclear missile has overshot the ship and is determined to be heading for land, a map on a computer display gives an indication of the missile's trajectory relative to the Nathan James and western Europe. After the nuclear detonation, an external shot shows the blast is to the port side of the ship, giving the impression the ship is on a southern bearing off the west coast of France. At the time of detonation, the bridge crew shield their eyes while facing the front of the bridge, which would give the impression the ship is pointed right at the blast rather than off the port side. Later, Master Chief Jeter reports that the jet stream is pushing the radiation north-northeast, as if to indicate the ship is currently sitting in the fallout zone, when this would actually be pushing the radiation cloud away from the Nathan James.
Revenge of the Rogues - S1-E10
Plot hole: During the fight at sundown, Cold gets a hit on Flash and he goes down. Eddie takes a shield and goes to help. But Flash was in the middle of the street with no obstacles around, and it's implausible that Eddie could have gotten to him without Cold or Heat seeing him.
The Protector of Concord Dawn - S2-E12
Plot hole: Sabine stowed away onboard the Phantom by hiding under the trapdoor in the shuttle's floor. That entry is just a single hatch, with nothing between it and the vacuum of space when the shuttle is flying. There is no way she could have hidden away there for the trip through hyperspace from the Phoenix Squadron fleet to Concord Dawn.
Plot hole: They need at least 12 magnets to make it work, Paige collected 11. (00:21:00 - 00:22:00)