I noticed next case.
Build some mine. For now for coal and copper appears the same behavior. Immediately after the mine is build(also once I didn't have free settler to work on the mine) I stopped the mine not to work(stop production button). After that clicked to upgrade the mine. Window with price appear, I click yes, window close and mine is not begin to upgrade. Upgrade button can not be clicked again. I log out, clear browser cache, login again and the mine is not started to upgrade. Now if I click to upgrade it work well and there is no problem.
Thanks