Not sure if I have the name exactly right, but I am referring to the merc that instantly swaps planets in the AOE where it plants a starbase.
It seems that the system treats this merc like a regular constructor if you have it stationed at a starbase. I tend to keep my mercs at a starbase near my home planet until I can organize them in a fleet. I also tend to save at the end of a turn, so I can pick up from more or less the same point when I return to a game. I will usually have a starbase or two that has unspent construction points, especially if I have used one of the mercs that has 5 or 10 free modules.
So what happened was I used the construction point from Swayer-11 at my home system starbase and did not notice it for several more saves (when I determined a system to hijack). It would be helpful to have a confirmation dialogue for that one especially valuable "constructor" to help guard against this happening to others. I can easily see how a confirmation for every constructor point would get tedious in a hurry, but again, I think this is a special case.
I will definitely not keep that merc at a starbase in the future.