Hi Stu,
I can explain what you’ve been charged.
Your £15.90 fare is made up of the zone 1-9 off-peak cap (£14.10) plus the £1.80 single fare from Brentwood to Shenfield. There is a £7.30 surcharge placed on peak journeys to/from Heathrow on the Elizabeth line, but the fare is included in caps. Shenfield benefits from the off-peak (after 0930) cap to zone 9 (Brentwood) being relatively cheap and a quite low fare between the last two stations.
The good news is that your wife’s card will be due a refund next time she uses it because her touches will have been run through the back office system and the charge recalculated. If she uses the card within the week after the refund has been queued then it will be added to her balance immediately. After that it will be added on the second touch.