Sometimes, we build an Item by slightly modifying  an already built item.
 
The BOM for this new item may have some items with a negative quantity because we remove something and put it back in stock.
 
In some cases, if a BOM has negative quantities, the "Maximum which can be built:" at the bottom of the report may show a negative number that does not seem to correlate to anything.
 
In addition, some of the negitive line items show as a shortage on the report.  No matter how may items are available for a negative line item, that line should never be flagged as a shortage since issuing the BOM will increase the on hand.