I found negative emission outputs  for the wind/grid-connected and wind/PV/grid connected system. I am confused whyit is like that??

After searching I found your below mentioned statement:

Sales of power to the grid result in reduced grid emissions, and HOMER credits the power system with these reductions. The system can even achieve negative emissions of one or more pollutants if it sells a lot of low-emissions electricity to the grid. 

Can you please explain this statement for my clarification?

Your system must be selling lots of power to the grid.  Here's the last paragraph of the help file article titled 'How HOMER Calculates Emissions':

Grid

In simulating a grid-connected system, HOMER calculates the net grid purchases, equal to the total grid purchases minus the total grid sales. To calculate the emissions of each pollutant associated with these net grid purchases, HOMER simply multiplies the net grid purchases (in kWh) by the emission factor (in g/kWh) for each pollutant. If the system sells more power to the grid than it buys from the grid over the year, the net grid purchases will be negative and so will the grid-related emissions of each pollutant.



Your system must have negative net grid purchases.  The product of that net grid purchases and the grid emissions factor must exceed the emissions of your systems' components.