If this really happen, you must have registered the same card at both programs, and timing was such that the first dine had already come in to the first program, then you registered at the second program, and then the second dine came in.

The way it works is that the program to which the card is associated at the time the dine comes in (which I think is typically a day before you see it online) is the one that's used.

I've certainly done this on purpose, when I had a promotion on a particular credit card, but which airline I wanted to earn changed from one month to the next as one lost its promo and the other gained a promo. With a couple day gap (during which it's sort of hard to predict which program a particular dine will credit to), I was able to move the card from the first program to the second program.

But the programs freak out if you remove all cards from a program. So it's best to always keep at least one card in each program. But if you wish, it can be cards that you have in a drawer but never use (since RN will never charge anything to the card). You also don't need to delete a card from an RN account just because the card is expired or cancelled; knowing this can help you always keep a card or two in each account, while also moving your favorite card between account to "follow the bonuses".