Long Stop Time: Not running script because past shutdown deadline

So I am getting tons of Not running script because past shutdown deadline errors in my console after the game stops in studio. I think this is causing the long stopping time. (Not my codebase btw, building on someone elses)

In every script where it says this, it has a while wait() loop.

Are the while wait() loops the problem, and if so why?

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This is likely to be related to this issue:

Yeah, I found a nasty wait statement in their bind to close. I fixed it.