LGA on the weekends can be a zoo. I often fly out of there early on weekdays, and it goes relatively smoothly as the number of frequent travelers is very high. On Fri-Sun, though, you get a much larger number of infrequent travelers. LGA (and NYNJPA, in general) is not the most user-friendly place, and it really is easy to get confused. On the flip-side, once one becomes adept at using LGA, it can be one of the most efficient airports in the country.
Personally, I think there is particular combination of personalities of New York metro residents that can make this worse, but that is just speculation on my part after having lived there for a number of years.