Steps for reproduce:
- build armored locomotive, and add plenty of expensive modules to grid
- remove it (by hand or with deconstruction planner)
- press Ctrl-Z

After that bots place locomotive and for second it show blue icon for not installed modules, than it disappear. All modules that was in locomotive grid is gone.

I tried to reproduce this, but the result is a bit different from yours:
- Same: the placed locomotive is empty (without any modules).
- Different: the "original" locomotive with modules is intact in player inventory.
Conclusion: The undo function placed the same type of locomotive, but without caring about the grid contents. The bots just placed whatever the same type of locomotive to the ghost.

But anyway, it seems the problem is about undo function and ghost blueprinting. They are both from the base game, and this mod have nothing to do with them.
Please report this to Factorio forum Bug Reports board.