In reviewing the schematic, I have found that the free wheel diodes seem to be connected incorrectly. The free wheel diodes are D1, D2 and D3 that are the 1n4004. These diodes are used to deal with inductive loads. Inductive loads, such as a relay coil, will want the current to keep flowing until the inductive energy within the load is dissipated. These diodes, as hooked up now, are not creating a path to deal with this energy. If an inductive load is used, most likely there will be a large voltage spike on the collector of the TIP50 transistors. V=L*dI/dT so the faster it is turned off, the higher the current or the larger the inductance the higher that spike will be.
If noise has been an issue for your system or your burning up PWM drivers this may be a major contributor.
I would recommend moving the diode or adding an additional diode. The hook-up would be anode the the TIP50 collector and cathode to Vss.
The existing diodes are fine where they are but aren't really doing anything.