The upgrade hotkey works different than when you manually click the upgrades:
Without hotkeys:
You have 4 t1 mexes. You select one and upgrade it. Now you select all 4 mex and click the upgrade button. Now all mexes will be upgrading.
With hotkeys:
You have 4 t1 mexes. You select one and upgrade it. Now you select all 4 mex and use the upgrade hotkey. Only the first mex is upgrading and the other 3 aren't.
I doubt this is intentional since it doesn't really make any sense.