Plot hole: When Indy is stepping on the letters at the end, trying to spell out God's name, he steps on J, incorrectly, causing it to collapse. When he falls through, however, he grabs onto another letter so as not to fall down. The letters he grabs onto and pulls himself up are an L and a Y, which are not in the word Iehova, so should have collapsed too. (01:46:20)
Plot hole: After Indy discovers the knight's tomb, the men after him light the petroleum and Jones dives under the liquid with the paper he used to copy the knight's shield. How could that paper have made it through that scene without gaining damage?