Hello!
I've noticed some few problems with Cybersyn and stations with repeated names.
Imagine your factory with hundreds of stations named "Provide" and "Request".
When Cybersyn (and I think LTN as well) want to send a train to a specific station, regardless of name, it first makes a coordinate destination (of the station) in the train's schedule, then the actual station. The train will go to the coordinate station, then the next stop is the target station, a feet in front of it. If Cybersyn didn't do this, the train would pick the nearest station with the same name and mix cargo.
The problems arrives with Train Upgrader is that it appears to inster the station after the train's current target station. If the train is going to a coordinate station and Train Upgrader decides to insert the Upgrade station right afterward, the train will arrive at the coordinates, but instead of stopping at the target station, will go to get upgraded, then head to the NEAREST station with the same name. This results in trains mixing cargos.
It would be better if the Train Upgrader mod worked in tandem with Cybersyn/LTN. One potential solution would be to only select trains who are currently waiting at a depot. Another solution would be to not request trains, but still put upgrader chests next to stations who will upgrade whatever trains end up stopping at it.
I may provide a world download if needed to reproduce the error.