I do not know if this is a bug, but very annoying anyway. City governor assigns workers as specialists, even thought there are other GP available (even engineers and priests).

I don't understand what you mean. What has assigning specialists to do with whether there are any GP (Great Person)? Maybe you could explain some more where you think the problem is.

For example when you switch to mercandilism, the free specialist that the governor assigns is a worker

I think the term you are looking for is 'citizen'.

Ah. Now I get it. You mean that the free sprecialist is assigned as a citizen instead of something more useful, like an engineer or priest?
Well, I do it manually, so I don't think I ever saw this happen but I agree that there is no reason to use a citizen when you can use an engineer or priest instead (+1 hammer for all of them plus additional benefits for engineer and priest).

Do you have a save, by any chance?