The ark gets opened and the evil spirits come out and kill everyone there except for Indy and Marion. Did the evil spirits not see them as they were tied up and away from where the ark was opened? Because they killed everyone on ground and then went back in the ark and shut the lid. And obviously there were nazis still left on the submarine. How did Indy and Marion make it back with the ark no less? Did I find 2 plot holes here?
I just always figured that Indy's ability to speak Hebrew was better than Belloq so he was able to nail the ritual the first time around. It's kind of like Army of Darkness... Belloq mispronounced something and, sure enough, all hell broke loose. Indy knew the mistake as soon as he heard it and that's how he knew to close his eyes. After that Indy simply went and used the correct words and was able to escape the island safely with the ark.
Wouldn't call those plot holes since it doesn't hurt the plot of the movie. At most I would say they are unanswered questions.
The first is actually answered in a deleted scene. When Indy and Sullah are showing the head piece to the old man the movie only shows where he reveals how tall the Staff of Ra has to be. In the deleted scenes he also warns Indy that anyone who touches the Ark, or looks upon it while it's open will die. That's how Indy knew to close his eyes.
As far as getting the Ark off the Island and back to the US, well Speilberg figured it was better for the flow of the movie not to show that, and let us decide for ourselves how they did it. Maybe they hid the Ark in a cave, then went back to the base, stole a boat, retrieved the Ark and somehow found passage back to the States. It's open for you to decide.