I haven't really been involved in tap on / tap off fares, but it's quite possible this is causing it.
It depends how the operator has set the two (or more) 'journeys' up in the ticketing system. Some operators set the end to end journey up as a single journey in their systems, but send an edited split version with their registrations - that probably works best for all practical purposes but may not be the officially correct way of doing it.
Others have it in systems as two separate journeys, so the driver might be entering a new route and / or journey number to the ticket machine at the split point, and if so, the kit on the bus will see it as two separate journeys.
Presume if 'tap off invalid' message is coming up, are you being charged a maximum fare for your journey? (or one for each 'incomplete' journey?)
Is the ticket scheme run by the operator or local authority? (or for that matter Welsh Government? I am out of touch with Wales)
Without knowing where or who the operator is, all I can suggest is have a look at their website and see if it says anything, failing that get in touch with operator (or council if it's their scheme) and ask what you're supposed to do.
The whole split registration thing is a bit of a bodge, and To-To may be a new can of worms for it.