I'm a US Citizen with Mexican residency. If I were to open a Mexican bank account, could I use my Mexican debit card in Cuba? Or would this somehow be traceable back to me when I re-enter the US, and get me into trouble there?
Long story short. I think what you're concerned about FATCA (Foreign Account Tax Compliance Act). The minimum amount required reportable by any foreign institution is $10,000, which means that if you keep under that amount in your Mexican account they technically don't have to report it but they still might anyway.
There is no requirement to report transactions on those accounts so your transactions in Cuba don't need to be reported to the US Government, whether or not they will find out about is a different story.