Plot hole: In one of the scenes where Jones and Del Toro are fighting hand to hand, Del Toro's knife is knocked into the bushes. They continue to fight until a point where Del Toro has gained the upper hand. Del Toro is on top of Jones, who is almost unconscious. Instead of finishing Jones off, Del Toro looks around for his knife. This doesn't make sense. Del Toro is a trained killer. He doesn't need a knife to kill Jones.
Plot hole: After the team takes care of the ethnic cleansers, there is a flat-bed lorry with a belt-fed weapon just sitting there. Since the cleansers came in from somewhere ahead of the team, why not load the refugees onto the truck and head out? If nothing else, it would increase their lead over the pursuers.
Plot hole: At the end of the film, Trevor McDonald reads the news and says "the spy, who we cannot name for legal reasons..." Yet on screen, one of the newspapers that flashes up (I think it's The Times), has a headline congratulating Johnny English by name. He's not going to be a secret spy for long if they reveal that.
Plot hole: In the shot near the end where Steven is fighting the Chinese guy, the Chinese guy fires an arrow at Steven and Steven picks up the Samurai, cutting it in half. This is impossible to do because arrows don't travel in a straight line, although the arrow in the film travels in a straight line.