An article posted on Ledgend of MI entitled "LeChuck's Life and Plot Holes of MI4" talks about exactly that. It was pointed out that this was a spoiler.. you should have completed it by now dammit!!! anyways highlight the text to read the quote
In MI4, you find out that Herman Toothrot (the hermit of Monkey Island) is actually Elaine's grandfather! How is this possible? You see, the story about how he got to Monkey Island contradicts the story he told Guybrush in the first game. I've narrowed it down to two possibilities..An interesting read, if rather nit picky.. i'd rather let sleeping dogs.. well you get the idea. Read it here.