My understanding is that this is because we bill by family and not student. We prefer to have parents pay activity fees via eFunds. If a parent pays 3 seasons of sports fees via eFunds prior to assigning the fees in FM eFunds then automatically assigns and pays the fee and then at a later time when we run the mass assign fee Utility the paid fees aren't recognized another (duplicate) fee is created and they now have unpaid fees. Using that same scenario and having the parents pay the fee with check or cash assign the fee manually and then later mass assign the fees in FM the paid fees are recognized and all is right in the world.
When this happened last year Skyward wrote a "fix" program for us which allow us to find where this happened and then had to manually correct. We have now stopped allowing parents to pay activity fees until they are assigned which has decreased eFunds usage.