It sounds like you haven't created a navmesh. Enemies like to run away from you when they can't get to you, and if there's no navmesh, they can't figure out how to get to you.
Wasn't that bad it looks good but i found that nearly every enemy just runs away from me before i even get to shoot them and also there are 2 unfinished areas where you can fall off the map >.> oh and the 2 glowing ghouls were just running into the corner and not even attacking me and the other 2 ghouls plus the super mutant had their backs turned and didn't attempt to attack me when i shot them.
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and add a few screenshots if you can i think this is quite intresting ">