I always thought that Neri,while a loyal soldier who didn't question orders,was disappointed in Mike when he gave the nod.
It looks like Neri's thinking,"I wish I didn't have to do this,but it's not my call".
My take is that he thought maybe Mike had mellowed a little and decided to forgive Fredo,only to find quite the opposite.
Also,I think Neri genuinely liked Fredo,and knew he was "dumb,like everyone says" and that Mike killing him was petty and vindictive.