Plot hole: Even if the white blood cells will attack and destroy the sub and the body of Doctor Martin the atoms would still remain and take normal size after the critical 1 hour is up. This would also apply to the laser gun which they forgot or left behind on purpose, as well as several dozen litres of saline solution which were miniaturised and pumped into Benes' body. He's in a lot of trouble.
Plot hole: After Blondie has "teamed up" with Angel Eyes, he hears a gunshot and says something like "Every gun sings its own tune", indicating that he's recognized the shot as being from Tuco's gun. But how did Tuco get his gun back? It certainly would have been confiscated when he entered the prison camp, and the chance that the guard on the train has that exact gun is extremely unlikely - he would most likely have had an officially issued sidearm.