Same problem here. The UI is misleading - it shows one indicator per line, but supports one bookmark per column.

I can imagine there are edge cases when somebody may want more than one bookmark per line, but if that's the case, the UI should really show bookmark exactly where it is, so it would be possible to toggle it without blindly guessing and ending up with 20 unwanted bookmarks on the same line :)

I wouldn't mind if it was just one bookmark per line (but remembering the column where it was set).