The mod "Single Train Unit" has a small double-ended train that essentially works as a very compact 1-1-1 (taking up only 6 tiles, one standard wagon length).
As I understand it, it actually spawns in three entities under the hood. Each are 2 tiles long.
Project Cybersyn's "Automatic allow-list" incorrectly identifies it being 3 wagons long, making short (1-wagon long) stations unusable. It also confuses combinators in "Wagon control" mode.
I assume similar issues will be present from other mods that add train wagons or locomotive of non-standard length.
Relevant mods in use:
-Project Cybersyn (of course)
-Editor extensions (for easy testing in map editor, used for infinite power and super inserters - https://mods.factorio.com/mod/EditorExtensions)
-Single Train Unit (the problematic wagon in question - https://mods.factorio.com/mod/single_train_unit)
Blueprint with repro-setup at:
https://hastebin.com/share/bocebogoxu.bash
1. Place down a double headed cargo train unit at the depot
2. Give it fuel and a schedule
You will notice that the cybernetic combinator in 'wagon control' mode for the SECOND wagon (which does not exist).
Only the middle two tiles seems to connect to the combinator, though even with a standard 1-1-1 in the same track I can't quite get it to behave as I'd expect. Either way it seems to be separate from this bug.
For further testing/details/effects:
1. Enable "Automatic allow-list" and before placing the train (or toggle to manual, remove schedule, empty it, and start it back at the depot)
You should now get errors about no matching trains
2. Place inserters where the second wagon would be (by both supply an request stations)
It should now run as expected.
Workarounds:
Disable "Automatic allow-list" and put all single unit trains into their own network.
That way your primary network can use the magic, and the single units get a network all to their own to avoid issues.