What would count as antimatter waste? Edit
I doubt it would be anything like "leftover antimatter," as the M/AM reaction has 100% efficiency. Could the waste be reactor components and related materials that have been irradiated by gamma radiation and other forms of energy produced by the reaction? I could imagine the actual reactor core and its coolants would end up as waste if they're not properly shielded. Or could it be from the actual creation of antimatter? We don't know what kind of anti-elements are used by the different civilizations in their M/AM cores. The Federation uses deuterium, so could some races use tritium or heavier elements and/or their respective isotopes? If certain antimatter fuels are made as certain isotopes, whose matter counterparts would be radioactive, then that would irradiate materials and equipment used in the creation of said fuels.