LTN train stations have two extra entities when you place them down. Those two entities disappear when the station is upgraded to a higher quality, breaking the station.

If it can't be fixed is there at least a way to stop just the LTN station from being upgraded automatically?

You have to add something to the "skipped_entities" list of the mod's Startup settings, but I don't know what it wants. I tried "logistic_train_station" which afaik, that is the name internally..

I was wrong, the actual name, "logistic-train-stop" works. Add it to the skipped_entities list and it ignores it just fine.