A lot of different things can be causing this. Here are a few:
You could be using the wrong type of paint brush. Make sure you are using a nylon brush for waterborne polyurethane and a natural bristle brush for oil-based polyurethane. Soak the brush in water before using and you will see bubbles coming out. Then cloth dry well before using.
You could be using too much finish or you could be overbrushing. Also, you should make sure yuo have ample ventillation to allow the solvents to escape the room.