Image manipulation can be a bit of a minefield with the vast number of applications handling image metadata differently.
I discovered some photos that were rotated using old software were being auto-rotated by XnView back to the wrong orientation. It turns out the software had rotated the images but failed to update the EXIF orientation value, so that XnView would rotate them again based on the old EXIF data.
It was a simple solution to reset the EXIF orientation data in all the photos, but now I’m aware to be more careful of which software I allow near my photos.