I would try removing the caulking around the shower pan and redo it. If that doesn't fix it, basically I would rebuild the whole shower. It looks like water might flow beneath the flooring here, which might cause a lot of problems in the future.
Also, I cant see it well in your pictures, but I've found in past remodelling projects that the best way to make showers leak free, is to first place the shower pan and then do the wall tiles, so the tiles are slightly above the pan.