Effect them how? Is it in the main display tank or an overflow box? Cleaning magnets would effect them as well. I don't have a pump, but do have a maganavore cleaning magnet. I keep it up out of the way in a corner. I have never noticed anything odd happening besides when I actually use it.
If you have some odd behavior I would tend to lean more toward a possible electrical motor problem. Add a ground probe to your tank just in case.