If you used Docker on your machine, this was a bug in the remount code (they forgot to re-trigger the qgroup scan if it was interrupted when you did an rw-remount) which I fixed several years ago[1]. I don't know what that will do for your confidence in btrfs, but hopefully it'll give you some closure.
[1]: https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/lin...