Thanks for the clarification but I actually understood you correctly the first time.
Actually, the civ5 API (the set of levers, pumps and wheels that mods can use to interact with the program) does not even contain a function to make civ5 aware of a resource without knowing the related tech so it should not be possible. However, it could be a side-effect, likely a bug, of something else and I see four candidates:
* The function to change a resource quantity, but it is used by IGE anytime you add/change/remove a resource, so I think we would have seen this bug already. There is a edge case where a luxury resource is replaced by a strategic resource but, even that, I already did it in some of my games.
* Some bug when a tile's owner change but it is used by IGE anytime you modify a tile (to circumvent a civ5 bug). So, if there was some side-effect, we would already definitely know it.
* The function to add free resources (add resources to your resource pool without adding a physical resource on a tile) but IGE does not use it.
* The functions to setup trade agreements but IGE does not use them.
So, yeah, I think it is very unlikely to come from IGE. If you actually use a mod that rely on the latter functions, they could be candidates. Or a buggy trainer.
Now, I cannot be 100% sure. Because the civ5 API is only partially documented and quite messy sometimes, with nasty hidden bugs and side-effects waiting around the corner. But, right now, I don't see anything that could cause it and I don't have any trail to investigate, I would need reproduction steps. Do you happen to remember what you did through IGE, i.e. what you changed ? If you only opened IGE and did not change anything, then it is safe to say that IGE is not the culprit.
Finally, aside of mods and trainers, it could also just be an instable memory, an electrical defect, or some electrons jumping from one transistor to another because of quantum effects (it happens a few times a year on every computer but is typically harmless): all of that can cause a 1 to become a 0 or vice-versa and cause a bug that will never appear again. This is the wonder land of "bugs we have no clue about them".