The issue is that you touched in at the gatelines for platforms 13/14. These are set up as if they were a completely separate station to the rest of Victoria NR, to facilitate the charging of a premium fare for Gatwick Express journeys.
Accordingly they also do not have an OSI to or from any other station or gateline, including the Underground gateline at Victoria. Therefore you are charged separately for each portion of your journey.
Of course this is not advertised anywhere and so TfL have indeed overcharged you, even if it makes sense by their internal rules.
What's supposed to happen is that if a non-GX service uses platforms 13/14, those gates are closed and passengers are redirected to use other entrances. Evidently that didn't happen in this case.