I am playing via the itch.io app, and also played it on mobile to try and reproduce the bug. It is still crashing on both for just those two levels. Only thing I could find that was the same on both files was I was researching late game things.
This is the one that happens on stage 4 arrival and recon below.
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ERROR in
action number 1
of Draw Event
for object CheckPoint:
DoAdd :2: Malformed variable
at gml_Object_CheckPoint_Draw_0
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gml_Object_CheckPoint_Draw_0 (line -1)