Yeah this happens to me sometimes too. Not all markers do this so I really have no idea what causes some to be visible.

For the stubborn ones, click on the marker in the editor and at the bottom, you see an opacity/transparency bar. Put it at zero (all the way to the left) and it will disappear.

If you want to find the marker later on, do yourself a favor and take a picture first. Remember it will also be invisible to you in the editor too.

This should not be happening.. do you have a repro mission by chance? When it happens is it the same marker(s) that are showing each time?

If the TAOR marker is not invisible, then it is not being recognized. Try renaming your TAOR and/or ensuring that the correct name is used.

If the issue persists, try reversing the size of your axes and rotating the marker by 90 degrees to compensate for the size change. This is an issue regarding a BIS function.

This has happened to me in every single mission I've ever made. That really means something is wrong? Hmmm. Had no clue.

Mine generally happen when I place two markers on eachother (ex. when adding a blacklist marker for the edges of the map so installations don't spawn off the grid, or creating a no Logistics support zone deep within the enemy AO, etc).. I believe this is the case in all occurrences actually.