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: Near the start of the film Tommy Lee Jones tracks a wounded wolf through the woods and removes a snare from its leg. The problem with this is there is no way he could have just walked up to a wild animal start touching it without it attacking. Plus this is a wounded animal which as anyone who deals with animals can tell you makes them twice as dangerous.