A purchase at the store can only be a single transaction. If it found a second card, it wouldn't have a transacation waiting for it.
I can see someone with their wallet, with 2 cards in in, waving it back and forth in front of a Presto reader, catching one card as it passes, and inadvertently passing it near a second time and grabbing a different one. Or passing it by so slowly, that it sees a second card a split-second later. People are funny and unpredictable.
On one occasion, I've already had a Presto reader get the same card twice - which is supposed to be impossible, as it's designed not to charge the same card a second time straight away. But there was this bizarre double beep, and when I checked later, Presto said it was a software problem that had just been introduced, and they were fixing. (it ended up tapping me on and then off in rapid procession ... this was a couple of years ago, never happened again).
I'd suggest simply taking the Presto card out of the wallet, if one has multiple RFID cards.