The station, when played, only works for one chunk of track. In the boardgame version, players usually move the station physically over the track being used, thus helping to visualize the "one, and only one"...
Note that, page 6 of the rules for TTR:Europe, the following:
If a player uses the same Station to help connect cities on several different Tickets, he must use the same route into the city with the Station for all
of those Tickets. The Train Station owner does not need to decide which route he will use until the end of the game.
So, in the case of the OP's issue, obviously, another route was used (probably for other tickets).
Having played both the computer version and the tabletop version, however, occasionally the computer version glitches on stations, using it for the lower value route.