Yes, that's the essence of what's (not) possible with train station circuits. You cannot directly distinguish between an (empty) train on the way to the station and a (full) train currently in the process of leaving the station but still on the stations' premises. When I realized this some time ...

I'm trying to set up a farm system on Gleba where the agriculture towers harvest if the total capacity of the trains incoming or already at the station is greater than the amount of fruit already stored at the train stop.

E.g., 2 trains on the way, total capacity = 16,000. Chests contents = 4,000 ...