It is frustrating when this happens. Most of the time it is worthwhile, but there are edge cases where it goes ‘wrong’. The good news is that you are free to use two cards if you want. You obviously lose the capping ability, but if you are just making one journey then it’s fine.
Other strategies that you can use are available. You can break the OSI by waiting 40 minutes at Paddington between touch out from the Underground and touch in on National Rail. You can also touch in on a bus and then get straight off. This costs £1.65 but avoids the wait.
You could also split at Ealing Broadway instead of Paddington which would be £3.60 peak plus £5.50 off-peak. You’d need to exit the station after getting off the Central Line and go straight back in. This one will also work when through Elizabeth line trains start running later in the year.
Hope this helps.