That bug is as old as the game. The players even have an affectionate name for it: phantom spoils. Sadly, it happens randomly (almost always on big accounts) and I never managed to get Plarium to reproduce it and admit that there is a problem. With time, I gave up, and I stopped counting on those res.

I asked again and this time I did get a bit more info. I won't go into technical details of what exactly is happening, but one can work around it this way: after collecting the resources, send some units to your harbour, or claim a reward for a quest/tournament, etc. These action will synchronise the data and the collected resources should be available for usage.

I know the feeling. That's why I simply don't count on that rum.

@Navigator: I get this when I try to respond to your PM:

You're unable to send messages to this user due to their privacy settings.