Alright I am able to reproduce Hector's replay, it looks like if you land the glider at the right spot it will block the building from upgrading (not 100% if this is causing it just my guess).
Sully, when you had this issue occur did you have a glider land near the building as well?
No, when it happened to me there were no gliders deployed at all. I simply upgraded either 5 man squads or AEC, then upgraded to tier 3. Once the tier 3 upgrade completed it was grayed out and red "Requires: no other upgrades" and no units were able to be built from the tier 3 structure.