Hello Craminu and welcome on CF.
1) In some circumstances, civ5 is unable to generate the terrain mesh during the reloading and freezes. Since the terrain generation is closed source, no one but Firaxis knows what its limits are.
2) I discovered one of those limits:
between every land tile and ocean tile, you must have a coastal tile.
3) I tried to make sure that IGE would always put coasts between land and ocean. It is possible that I have forgotten one edge case, allowing you to circumvent this safety hack.
4) Therefore you may have found a way to put ocean tiles right next to land tiles, or hit any other limit that the mesh generation algorithm has. This can cause civ5 to freeze.
If you ever find reproduction steps so that we can assert whether it was caused by IGE or not, and how it happens, I would be very grateful to you and would prevent this to happen again. But right now the only things I can say are:
* I do not know whether it was triggered by IGE or not (it could be a civ5 bug after all)
* If you can still abuse IGE, at least it is very rare.
* Beware whenever you edit the coastal line.