There is an extra iron and marble deposit (and, less importantly, a stone one) that your geologist isn't allowed to discover even when you've gained possession of the whole island. If you try it simply tells you that you have enough of that type already.
The extra marble one is in zone 1 and the geologist will sometimes alternate between the two that are there, but will never be allowed to discover both at the same time. The iron one is in zone 5 where there are 3 deposits but, again, only 2 are allowed, leaving the extra one sitting there undiscoverable!
Why is this? If they're there, let us have em!