I have 2 Citi credit cards for 2 different merchants. Quicken mixes them up

What do you mean by "2 different merchants"?

Cards are issued by the bank, Citi in this case, and can almost always be used at any merchant.

Perhaps do you mean that they're co-branded by different merchants, but can still be used anywhere? For example, I have Chase cards for both Southwest Airlines and Marriott, but I can use them interchangeably … including using the Marriott card to buy Southwest tickets.

And, regarding the mix-up, does it happen sometimes, or all the time. If all the time, that would indicate that when you were setting them up in Q, you linked Card A at Citi with account B in Q and vice-versa.

If only sometimes, please do TOOLS, Account List and tell us what's in the "Transaction Download" column next to each of these accounts … and also what's in the Financial Institution column for each.