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Geologist Bug
I had two exhausted copper mines and sent two geologists to find new copper deposits and they found them in the spots two of the exhausted mines were at the time and the deposits were then full but it removed my mines and did not increase my building license count by two to account for removed buildings. The bug is that even though the mines were removed by the geologist's discovery it did not count the buildings as removed/ torn down and the building count remained the same as before the two mine were removed.
Two building license spots are now permanently used up without having buildings to show for it.