It seems to be more of an oversight than a bug per se and can easily be reproduced:

In the inserter and belt UI one can press the "logistic network" button (on the top right) to allow the machine to read contents of logistic network remotly and have logic implemented based on its contents ...

Wouldn't it then be better to remove the broken functionality entirely? As in either:

disable the ctrl-z functionality after pasting stations
or
disable the feature where the train's schedule changes automatically upon pasting station settings.

I never found this feature (trains auto-changing ...

A simple, easy to reproduce inconsistency within game's logic.

How to reproduce:
1. Create a rail with stations A and B at the ends.
2. Set a train to automatically travel between them (A -> B).
3. Copy train station A onto train station B. At this point in the train's schedule (automatically ...