I think I know what you're talking about. If the water runs down the side where the intake tube is on and not down the outlet, then it is time to clean your filter. This happened to me too, but I got rid of the backflow like this: First, get a bowl of tank water and rinse the filter pad in said bowl. Next, take the whole filter apart and thoroughly clean the inside of the box with a paper towel. You might want to also clean the part where the tube goes into the filter and allows the impeller to pump water.
I hope this helps.