Have exactly the same problem. I was actually adding 150m to each team when it happened, but having read "webeto"'s post I just went in to look, came out, and loans disappeared.
I can honestly say that I have never had any problem with the in - game editor since it was first launched many years ago. Together with a first ever error with the pre-game editor (Editor crashes when trying to mass remove loans etc) it makes me wonder if all the focus this year has been on the game itself - at the expense of the editors?
Edit: Just tried adding the monthly payments (Calculated) where there are none and it prevents the loans from being removed.