Hello.
I'm using v1.4.8.2 on minecraft v1.12, but I also seem to have the issue of entities spawning twice, whether generated by the /summon spawn script, or when the entities are pre-generated. For example, chests spawn twice, breaking a copy and scattering the contents, item frames are copied, and mobs spawn twice, with one version seeming to fall through the floor, so they appear on the bottommost level. This happens with vanilla and modded entities.

Never mind, I was just loading two overlapping instances of the same structure.... That's what I get for doing stuff at 2 am