If you have a blueprint that demands MU locomotives, that can cause the problem you are seeing. I'm not sure why you would have such a blueprint.
This is interesting. I make train blueprints by placing trains, dialing up the schedules, and then copying them into blueprints once I'm satisfied. Since the placed trains are already MU trains, then MU trains are now in the blueprints. I'm not sure how else I could work actually.
If you mouse over the ghost locomotives, are they called "MU Locomotive"?
Yes.
When you first drag the blueprint tool, it has the MU icon in the selection, but when the blueprint editor window opens, my mod replaces them with normal locomotives. Bots place normal locomotives, and they are converted to MU locomotives immediately after both are placed, and the train schedules are preserved.
Ah, now I understand what you meant when you said I shouldn't have such a blueprint. What you describe here is not the behavior I'm seeing:
https://factoriobin.com/post/fNDUpXsa
Can you post your save? There might be another mod interfering.
Very possible. As I mentioned in my previous comment, I feel like the onus is on me to do the binary search with disabling my own mods. But since you asked, here it is: https://transfer.sh/L9Ijss/uu.zip