The MU Control mod makes double-headed trains more realistic by allowing reversed engines to contribute to power. But to make that work efficiently in the factorio engine, it replaces all forward-backward engine pairs with different entities that are clones of the originals but have their acceleration doubled.
When the second Armored Locomotive of a pair is placed, the mod automatically replaces both with MU Armored Locomotives, which Rubia then appears to deconstruct (leaving an armored locomotive on the ground marked for deconstruction).
MU Control allows blacklisting entities from its scripts so this isn't causing crashes or making it impossible to do anything. However the high weight of wagons means realistic train behavior will be nice for outposting when I return to scale up the planet.
Edit to add: thank you for this mod. I appreciate your commitment to your vision and the result was a very fun and engaging logistics puzzle. I'm sure there's a bit more to come still as well ;). When I first played Cerys I was turned off by how grindy it was, but the progression here was smooth and rewarding the whole way through, plus the funny tidbits provide entertainment and don't overstay their welcome. I tried to find a recording of the song online but couldn't find anything playable. (One website claimed to have it, but refuses to play it.) Have you released it anywhere? I could rip the file out of the assets mod but that feels a bit icky, assuming you'd get something from listens on a real platform.