Next time you are in-game and see a [DEV] in chat let them know what happened and they can send you resources to compensate. Or we might be able to send you a bonus code if you prefer.
For your home city 5k is the basic storage without buildings or bonuses taken into account. It's possible the buildings were slow to load and weren't counted towards the cap. We'll see what we can do to stop this from happening in the future.