When I have both bottleneck and factorissimo installed the icons that show the color are not appearing inside the factory but somewhere random on the map, it may have to do with how factorissimo works but the floating random lights in the middle of nowhere are rather weird.

I don't think I know how to fix this. It isn't surprising that factorissimo does some pretty funky stuff, and I am not sure I understand it well enough to fix this. Sorry.

My first guess would be make sure you are using any surface based versions of API features. If for example your lights are getting just coordinates, and assuming they belong on the Nauvis (overworld) surface that could explain OP's observed bug.

My understanding of modding best practices is that you should always use the surface aware API stuff unless you are absolutely sure Nauvis is the only surface your mod will need coords for.

Edit: And I go over to the GitHub and much savvier heads than mine have discussed and solved the problem. Props to Rseding91 for being awesome.

Try the new version, which I just uploaded. It might do the trick, though I haven't tested it against factorissimo.