Lets say that you have a wormhole where both ends are attractive. Here an object starts far away from rest, accelerates towards the wormholes mouth, travels through the throat at a small fraction of light, then come out the other end and decelerates as you travel away. Now lets say someone "clogs" the wormhole by dumping lots of matter into the wormhole through both ends at once, resulting in the matter staying inside. This would make safely travelling through the wormhole impossible as any ship that passed thorugh would burn up like a sattelite falling from orbit. How would someone "unclog" the wormhole and make it safe to travel through?
Dump antimatter "cleansing agent"
Provided you can accurately measure how much matter is clogging your wormhole, you just need to add the same amount of antimatter. The two will annihilate, and the resultant gamma radiation will escape the wormhole leaving it nice and clean.
Flush it out
Alternatively just giving it a good relativistic hosing down with regular matter may do the trick too: part of the momentum of the additional material will be transferred to the matter clogging the wormhole and bring it out to a distance where it can be captured. Repeat the process until the wormhole is sufficiently clean.