Thanks for the update.
You didn’t exceed the maximum journey time. The TfL website says that 90 minutes is allowed for a journey in zone 1 only. Can you reply back to them and dispute their assertion? The webpage is https://tfl.gov.uk/fares/how-to-pay-and-where-to-buy-tickets-and-oyster/pay-as-you-go/keep-within-maximum-journey-times.