I think the disappearing upgrades happend on the normal gatehouses too, aside from that the normal gates worked fine.
Another thing that might be of interest although I don't know if it is related:
After I first noticed the stuck construction of my first upgrade attempt I relogged, when I got back into my city the whole construction site of the advanced gate was just gone. I triggered the upgrade again it got stuck again, this time immediatly. Then I tried relogging again,
and my city crashed on load. It only started to work again with patch 1.05 B, which luckily came later on the very same day. (Thank you guys