It's those repeating sections and tables that are likely causing the trouble.
Again, if you right-click in the blue section you'll see a context menu appear with commands like "Insert ..." and "Remove ..." Those "..." parts of the menu item will indicate what repeating table/section(s) are the problem.
Most schemas have a "group" that contains the "repeating group", such as:
Root
--Group1
----Group2 (repeating)
------Field(s)
If you place your Group2 inside a section bound to Group1 then the Group2 commands will bubble up to Group1 and then stop there... otherwise they'll bubble up to Root--which is where you are getting your problem from.