I have two monitors that are connected to my laptop. I rotated the one on the left using the displays section of Settings. My laptop display is HIDPI so I had to use xrandr to scale both external monitors, like this:
xrandr --output DP-1-2-1 --scale 2x2
I'd guess that this is because the computer still thinks that my display is the width it was before scaling, but now that it has more pixels it hasn't accounted for that when positioning the displays, although I don't have this issue with the display on the right. I tested it with the display not rotated and I still had the issue. How can I fix this?
Installing arandr and opening it showed the overlapping displays, I was able to move them and export a shell script that fixes it.