Heh, when I read the symptoms:

“Some exhibited “haunted” behavior, seemingly jumping to random sections of the mcu program code, outputting messages on the display that made no sense given the context. One of them appeared to work in slow motion, with LED blinking and display updates noticeably more sluggish than normal,”

my first thought was that it smelled like a clock issue.

Some of the nastier issues I have had the pleasure to debug included (a) traces that had microcracks which affected analog readings when the PCB heated up after prolonged usage (QC issue from the PCB fab) and (b) a (suspected) ESD strike that gradually took out several components in the weeks following as I was investigating the device while new problems kept popping up. Marginally stable composite amplifiers have also caused some headaches over the years.

Hardware really is hard.