Thanks for all the replies. I think I might drill a small hole just to check for water. It sounds like I may not have a water problem if I don't see any water come out. When I took out the window and door handle, all the interior filler was solid around these places. I started looking at other door fixes on this site (thanks Brandy), by taking it apart, and it looked like it was evident that water and damage had been done in these area's.
Concerning the hinges, the holes were originally re-drilled into the trailer and not lined up correctly. Since I have the liner out, I put in a couple of extra layers of
fiberglass in this area to reinforce it and will put the holes in a different spot.