It clearly took the Swansea District Line if it missed Neath as well as Swansea. Maybe the line immediately west of Swansea was closed, so the only way it could get to Carmarthen was along the District Line?
Possibly. That would explain how other trains like the high speed
FGW▸ from Swansea to London Paddington were stopping at Neath.
I asked the station staff out of interest and they also didnt seem to understand why some trains stopped at Neath and Swansea and some didnt.