Something very similar occurred to me earlier today as well. I payed the resources necessary to upgrade my gold smelter from level 8 to level 10. I know for a fact that the upgrade had started because the progress bar was at 2% to level 9 when I logged off. When I returned a couple hours later my gold smelter was still at level 8, it was no longer in the processes of upgrading and all of the resources I spent to upgrade it to level 10 were not returned. Basically, it seems as if the upgrades were canceled, but my resources were never returned.
Currently I am completely unable to upgrade my gold smelter. I have the resources necessary and meet the prerequisites to upgrade the building, but when I select the option to upgrade nothing happens. I'm not sure if it matters, but I play the game on Kongregate.