Start by updating to KiCad V6.0.5.
Increments in the third digit are bug fixes, and there have been quite a few of those in the last half year, and upgrades should always be safe.
You could try sifting through the release notes and git commits and close issues to check whether this particular thing is fixed, but it’s unlikely to be worth the effort to do so.
I did a quick test in KiCad V6.0.5 and it appears to work as expected.
When that didn’t fix it I looked harder and discovered I had simply made a very stupid mistake and selected an exactly aligned F.Cu pad instead of the B.Cu pad I thought I had. Sorry for posting too quickly.