Interesting, I was able to fix my problem, but I'm not sure if using multi track bin files or deleting old saves is what fixed the issue. Going based off of what you have mentioned, I'm leaning more towards deleting old saves from the ps4 itself being the solution, because I use the same id from saturn games when making a fpkg.I actually combined mine due to having errors on a couple games that work (Astal/EJ2) and those fixed it, so I decided to combine all them all with CDmage like I did for the Switch nsps I made, and no more issue. It sounds like that could be the issue.
I do have another question if you can answer it. Do multi disc games have to use the same id? Because if they do and there is indeed a save bug, this may be a problem for anyone wanting to use multi disc games with the save state feature. It's not worst thing ever if it does, but it would suck.