As per practically every incident the core problem is communication.
Additional stop orders were originally in place for Bath & Chippenham on 1A58 (due to the crew shortages and trains were starting at Swindon and a 2-hour gap in service), but the train was apparently by the point of Bath severely overcrowded (the fact it seeminly lost minutes 7-8 minutes there would suggest so, even accounting for the additional stop), so the crew insisted Chippenham & Swindon (Can't see this being originally in the plan, so there was definitely confusion between control / crews / stations at some point) were then removed. I'm not surprised with it being that busy as a W. Country train arriving into Paddington in the late evening on a Sunday (even if it is October now).
Obviously with the chopping and changing, that's led to confusion although from what I've heard the crew made announcements although it was not heard in every carriage, which may be a fault with the PA. As with other passcom 'exponential problems', the overcrowding of the train made it harder to reset them, and the continued waiting lead to more passcoms etc. Train terminated at Reading which had its own problems and caused concerns over platform overcrowding there and another 387 was deployed to move passengers onwards.
Ultimately GWR's weekend shortages of high-speed crew aren't getting much better right now, and I'd be surprised if they improved substantially before Christmas.