I've noticed quite a few times then I click on teleport to Avery's court ( or somewhere else) some times a mark appears where I don't want it to causing an important mark to vanish. meaning I have to walk all the way back ( especially a pain when in a different world.)
I don't know is this is intentional or not so if anyone else is having the same problem feel free to post.
As I understand it, almost any time you teleport using the button to go to Avery's Court or the go to the location of a Friend in the Friend's Menu, you will set a Mark so you can easily return to where you teleported from. This is not a problem but the way it was designed.
Maybe, if a new Mark is replacing a current Mark, Pirate101 could ask if you want to destroy the old Mark with a brief description where the old Mark is pointing to. Also, there are some places (such as most dungeons), where a Mark cannot be set.
As far as I know, if you have a mark set somewhere else when you teleport to Avery's Court, that mark will stay where it is. If you do not have a mark set, one will appear where you were. I have never had a mark change from a place where I had it to a new place, unless I click the 'set mark' button. Perhaps you didn't have a mark set in the first place?