Running the Reconcile will look at the Purchasing records, the Sales records and Inventory records and will attempt to determine the correct value for the Allocation field. This situation happens pretty regularly with GP when Sales Orders are started, held for a while and then either forgotten as ORDERS or deleted days later. During which time changes in the Purchase data for an item will change the values on hand and that is where the fun starts. The Negative Allocation often is just a 'temporary state' as you know you can not allocate a negative amount. Follow the suggestion from Jorge, run the Reconile on the inventory - you can restrict ( I believe ) to a single item - it should remove the Negative Allocation.
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