After some hours of research i will finally post here :)
My problem is that I am not able to receive any MouseEvents on newly instantiated prefabs unless i modify them in any way in the unity editor while the game is running. I've already checked possible issues with UI but I can exclude that.
Prefab looks like that:
Script on the Prefab (EntityHandler deriving from MonoBehaviour):
Is there anything the internet didnt tell me yet or am I just blind? Any suggestions appreciated :)