It happens, it's dumb, but good luck finding a toilet that will fully cover the hole. Maybe it's time to put in some new tile! Finding the same tile to fill that area in is unlikely, unless you have some spares stocked away. Can't tell, but is it installed directly on the plywood? Generally, that's not an approved method, either. Well, there is one method, but it requires two layers of ply, properly installed, and a highly modified thinset which you probably don't have there.