Ah yes, the great fun of bug-hunting.
Probably most people in working IT have some stories to tell about this.
One thing that comes to my mind happened in a company where they used a simple software to create medical reports.
One clerk suddenly started creating "broken" PDF files.
I debugged this for hours and could not find anything.
At some point, I just copied the full raw text content that the clerk had written into one of those files out of the database into Sublime Text and I suddenly saw a small box appear between two characters of one word.
It turned out that this clerk had created a Word document with text templates.
Some of those texts were copied (at least partially) from other documents or websites.
Apparently, either something went wrong while copying some text, or there was some control-character embedded for whatever reason in that text.
I don't even remember what we did to prevent this from happening anymore, but one single "invisible" character can really cause a lot of trouble.
Another point is of course if you have strange side-effects just by combining specific software.
Back in the day when Crysis 1 was new and popular, I was a little involved in the modding-scene.
At some point, my CryEngine editor would refuse to start up.
I reinstalled it and tried to debug it, but I could not find anything myself.
So I turned to the forums and found a thread where a small group of people had the exact same problem. We all shared our setups and - basically by accident - found out that we all had Wacom tablets plugged-in to our computers.
I don't remember if it was enough to unplug the devices or if we also had to uninstall the Wacom drivers, but one of those things fixed the issue and we could all continue to build beautiful maps in the CryEngine.
Btw, I am now suddenly constantly aware of my Grammarly plugin ...