Hello Akutou and thank you for the report. You were totally right regarding the "tile acquired" event. Actually, IGE explictly does it in order to circumvent another bug (adding marble on a tile you owned does not grant marble to the city or civ). Now, unfortunately, this workaround can in turn cause bugs. It was already known for improvements (now fixed: improvements no longer trigger this event), seems like you just spotted another one for features and resources.
Unfortunately, as you can guess, there is just no solution for resources, I have to choose between one of those two civ5 bugs. Which do you prefer? Charybdis or Scylla? Maybe I can fix the problem for features, though, if the event is not required for them. I will investigate that and test how civ5 behaves when a savegame is reloaded in order to understand what's the most acceptable of the two bugs.
Regarding the location of IGE, unfortunately, there is no good solution, it's always bad for someone depending on other mods and the resolution. I encourage you to change its position according to your needs, see the first post to know how to do that.