If it really was a "small" duffle, then it should have fit under the seat. What you have described (larger bag in overhead bin, personal item under your seat) I've heard from FAs time and time again. I usually carry on a truly small duffle (it even fits under the seat in an RJ-145) and my laptop case. Any additional luggage gets checked. I occasionally place both carry on items in the overhead bin and have never heard an FA complain, but that may be because my two pieces combined take up less space than most rollaboards.