welcome - this can happen but it is unusual, it means that the product you are assessing is overall good for the environment (reduces emissions, produces resources). You will have negative results from
- system expansion modeling
- recycling and waste treatment modeling possibly
- omission / no consideration of flows that have impact in the impact assessment (so, the amount of your impacts is low and negative because the typically much higher "normal" impacts are not considered)
- incorrect specifcation of impact assessment methods
and maybe more.
Maybe you can post an example here?