2 big issues, dunno if they were reported before:
-If you cancel the construction of structures you build on settlements/econ plots (outside) you don't get your money back
-If you retreat units in a mine (dwarves) built on a settlement/econ plot (outside) and then sell it, the econ plot still think it belong to you (still your color, wich can prevent ennemy to take it) until you exit those units from the mine network