case 1:
If you encapsuled the game, then you need to create the save path folders before that - because the computer will not get permission to create the save folders inside an encapsuled program (which is something he would do automatically without encapsulation)
case 2:
depending on how you configured yanflys save core, it might need the correct path created as well. that completely depends on configuration of the plugin however, it does give additional options after all.
case 3:
your friend stored the game into a folder with special functions. That might restrict permissions even if neither of you did anything else.But it completely depends on what that path is and you would have to ask him for that.
case 4:
there is an old problem that prevented saves on maps with looping animations. It should be solved by now, but if you had an old project and never updated it it might still have that problem.