Muscle imbalances can have different causes, but a couple of the big ones are posture and work. A quick evaluation of your posture during various activities will point out if a problem lies there or not. Work plays a big part of you are often doing physical activities that favor one side of the body over another. To remedy the work situation, you could try alternating sides, but that may not always be possible. If neither of these help, then there are two popular methods of making both sides of the body equal.
The two popular methods involve modifying your training routines slightly. The first method is to work both sides to failure for the weaker side - the stronger side will still be able to do more, but it gives the weaker side a chance to catch up. The second method is to do everything normal, but to also add an extra set on the weaker side. Which you choose will depend primarily on how much energy/time you have for your workout.