Omg, I already have a name here lol thanks @Clousinators xD
I have seen this one before. I noticed it's usually caused by a wall on the floor below, combined with the use of platforms.
The 'easy and fast' way to try to fix this for me, would be to try to use a half wall (this setup makes me think that the EA calculator sets the walls as too high in some way, so you'd have to 'lower' them)
However, if you upload the build for me, I'm more than willing to take a closer look at it :)
Edit:
another fast solution: increase platform height on your top floor until the 'phantom shadows' are gone ;-) You might need to increase the level height to keep functionality.
Made you a
video elaborating on this issue :)