Has anyone had a problem using or changing U.S. dollars with marks on them (like pen marks, ink stamps etc)?

No problems. I usually just find an ATM when I get to my destination.

Not only can there be a problem with foreign money that's not pristine, Mexicans scrutinize every peso note as well. The teeniest tear can mean the bill will be rejected.

I suggest using the ATM when the bank is open. That way you can go in and change large bills for smaller ones, and unattractive bills for better ones.

Bixaorellana is correct. I scan my bills before going as anything that is marked on, torn, or that looks irregular will be rejected. If you use the ATM for pesos when you get there it will frequently give out large peso notes that no one wants as payment. I'm talking 500 pesos notes and above. I usually stop at the cambio if I have one and ask them to exchange it for smaller bills. Sometimes the lines at the bank are too long just to change bills. The cambio on the street will do it much quicker.

When you use the ATM, enter an amount that is not divisible by 500, like 4,800 pesos, then you will get some smaller bills. Many ATMs have a sign saying what denominations the machine has in it and also on the screen it will say what the smallest amount it will deliver.

I primarily use an ATM to get peso direct, and then break the 500 or 1000 notes one at a time at the hotel front desk, a busy restaurant, large grocery store.

At the cambio, no I haven't had USD refused myself, but I did make sure none were terribly torn or tattered.

We watched our Zihua bartender accept a nice tip one evening and, after the guest walked off, realized that she (the bartender) was quite upset. The guest had left her with ten worn US single dollar bills. She said they were basically useless to her because the bills were so worn that she wasn't going to be able to use them. We traded her for pesos and learned that US bils are okay for tips, but only if they are crisp and clean.