Not really, unless you create so much current that your fish wear themselves out swimming against it. Not usually a problem with big fish, but with small delicate fish like guppys and bettas you can set up too much current in the tank for them to handle.
Having extra filters isn't a problem in itself, like Ziggy2 said they will just grow the amount of bacteria to suit the bioload, if it's only 1/4 the max the filter could physically support thats not a problem.
Cheers
Ian