The reason those equal but opposite loads are there is because the individual members in the wall will have that force imposed on them as well as the components and cladding. While this is not important to your base reactions, it is important to the structure. The two programs are probably...
You should alert the engineer who did the design first and give them a chance to defend their design. It might be that they were not aware of the mistakes. Then you should take further steps if the engineer is unwilling to cooperate.
