In my map I have two units that can't be upgraded to another tower once they did damage. When I upgrade them before they attacked anything it works just fine but afterwards it's bugged. When you click the upgrade ability the mineral costs are gone but you get them back when you click the stop button on the building
They are called Short Circuit and Little Bird
Ehm, I have not downloaded your map, but from your description of the issue, I think the problem comes from your tower's attack. Am I right if I say these towers have specific and original attacks ?
You should take a look at validators too.