Plot hole: Even if the white blood cells will attack and destroy the sub and the body of Doctor Michaels 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. (02:02:52)
Suggested correction: There's a mistake in the question. It was Blondie who said that quote, not Angel Eyes. The question assumes Blondie was referring to the sound of the gunshots. It's more likely he was referring to the cadence of them. Tuco fired with a particular rhythm that Blondie came to recognise. Considered from this perspective it all makes sense.
Suggested correction: It's the type of gun Tuco likes that makes that particular sound.
Plot hole: Sir Rodney Ffing knows Jacqueline's name despite the fact that when the two of them first met, she never told him what her name was.