I have also had this problem. I have been careful not to leave a city in regions before the construction costs disappear on the stats page just to make sure they don't linger, therefore the problem isn't related to construction. I also have regional consumption on resources that no building in the game consumes, such as bricks.
This means that we can rule out structure consumption as well. The only other method of resource loss that I know of is decay from resources over their cap. I also gifted over my cap before I had built the proper storage and now when I have built my storage my resources are still draining.
There may be something else at work here though, as all resources are not draining at the same rate. Maybe it's multiplied by how many cities you visited, I don't know. All I do know, is that there is a strange decay happening over regional that doesn't apply to all resources the same way, even amongst those being effected by it.
I hope this can be fixed pronto, because drains like these would render small colonies unplayable simply because they can't outpace the decay.
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