Well without a capx its hard to see what the hell going on behind the scene btw Ive notice a couple of bugs such as the right outer wall the same object that let you go outside to the right its disappearing on load. most likely a z order bug.
This is my theory on your bug it might be that Even if you time scale the events to be 0 any event condition that is true during the pausing will pass on through such as movement of character bullet flying on the resume of the pause.
Oh another thing to be on aware is that all game redraw character at a pixel by pixel so it quite possible that you have a round object for your player that would corner clip things and get stuck Ive had that issue and what i did is that i made sure that everything was square off completely and no event of any strange angle.
Only thing i can think of to fix this id would make the save on the bed such as instead of dynamically make time go faster while in bed make it so it can fast forward time based on your choice such as do you want to sleep for 1 hr 3 hr 5 hr 10 hrs or save the game. Thus you can avoid this bug. and there is no movement after effect for your character that just my idea.
Another thing is that I can talk a merchant and then leave without closing the shop window but problem is when i leave the merchant i cannot close the menu unless if i talk to the merchant again.
Also the Left doorway does not open unless if that mean I need a key for it ?