Nahema: For me it looks like this:
In GOG Galaxy under Control / Overview, it states: reached 100%, same as in Activity Feed on GOG website user profile.
In GOG Galaxy under Control / My Progress it states 99% although all achievement "icons" are lit.
And on the GOG website under Profile / Games it states 98% in the game section....
I haven't played Control recently but I've got exactly the same problem with a game I played few days ago and where I unlocked the last achievement but the progress was stuck at 99%. Then it continued in another game where I earned one achievement but the progress was and still is at 0%.
So it seems to be a global problem with achievements. I contacted GOG support about it a week ago but still haven't received any reply.