Music elements visually misplaced and may not be fixed

I've been working on a 30+ page score with multiple pianos for at least a couple of months now and have recently came across a visual and audio-affecting bug that breaks a few musical elements.
This problem misplaces/shifts these elements back an entire beat or two, which affects how the MIDI plays it and how the score looks.
I've tried many solutions like reloading the score, the program, and trying to replace some of the broken/misplaced elements to no avail.
No amount of saving or replacing these elements fixes the problem, which somehow worsens each time I open the score.
Is this truly just a bug, or is my score now corrupted with bugs?
These are the bugged/misplaced elements in question.

Hairpins (Cresc., Dim.)
Ottavas (8va, 15ma)
Pedal Segments
Key Signatures
Clefs
Slurs

In the score, the problem starts at measure 89, at a second ending measure with a 3/4 time signature. There are a lot of invisible elements, all of the pedal segments in the measures after 89 all should be on the first beat, but are now misaligned.
If it's still not clear enough to see the discrepancies, there are some red notes highlighted, and some notes very high up in the ledger lines due to misplaced clefs too.
The audio also sounds weird at times when playing due to the misplaced ottavas and hairpins, which screws up playback from the MIDI
It's hard to describe, but the only way to describe and tell what the problem is if you look at measure 89, memorize the position of the hairpins and pedal markings, then reload the score to see if anything changed in that measure without tampering with the score at all. (ex, ottavas, pedal markings, hairpins are misplaced even more by multiple beats)

I haven't seen anyone with this kind of problem and I'm scared about the amount of work I'll lose.
Any little amount of feedback on this is greatly appreciated.
Thank you.