If sonication is not done carefully, the sample can become quite warm. This could cause proteases in the sample to increase their activity and degrade your protein. A method of cell breakage other than sonication that does not warm the sample (detergent lysis or French press, for example) might give better results. If you want to still use sonication, use short bursts with long periods of cooling between, keeping the sample on ice throughout, and include a protease inhibitor cocktail.
Probably Adam B Shapiro is right and you have to optimize the lysis by using a more gentle sonication or other exctraction method however it is difficult to provide a real answer without see the gels.