@tech_support,
If you use the right-click menu option to clean up blocks, and you have comments connected to some blocks, and some of those blocks are moved in the clean up process, then those comments stay at their original position and don’t move relative to the blocks they are connected to. You can see this by switching to sprites and back again - or by saving and reloading.
It makes a mess, if you have a lot of comments. Every comment has to be manually re-adjusted to fix it.