Initially, I believe this is a case in which quantities are being overridden. This means, the system allows to enter "out" transactions even if there is no balance to cover the quantity out. This could occurs form Sales or Inventory module. If this is the reason, and it is not an accepted scenario in your company, make sure to prevent override quantity from the setup level.
As for the inventory reconciliation, such override records are created perfectly in your inventory module, Dynamics GP creates a "dummy" cost layer in IV10200 for the associated override document in IV10201 with a zero quantity received. This means, you may find records in IV10200 which have 0 Quantity Received and an actual quantity under the field quantity sold. This record is flagged in the HITB table (SEE30303) with a value of 1 under the field "IsOverride".
Inventory reconciliation calculates the sum of all sold transactions from IV1021 and make sure that they are equal to the summary quantity sold value in IV10200 according to a specific receipt sequence relationship. You may want to take a look at the following articles as related to inventory reconciliation flow and override documents.
Your feedback is highly appreciated,