The negative sign represents that the treatment activity is supplying the service of removing a certain mass of the reference product for treatment (either final disposal or recycling). The reference product is physically an input to the treatment activity, but since the reference product is placed on the output side, it needs the negative sign to maintain the mass balance of the activity. The by-products of the treatment activity (with positive sign) represent the recycled products after treatment.
For more information on the linking process in the APOS system model (former Allocation, ecoinvent default) and Consequential system model see:
Allocation at the Point of Substitution
Linking in the Consequential System Model