Back on topic...
As many have already posted, if as the receiver you're sure that a serve was in but your partner called it out, you should overrule your partner immediately. However this is not the situation here, since you're not sure either way but just have some doubts.
How about asking your partner, after some of these calls, something along the lines of "I was so intent on the return that I didn't even see where it landed! How much did it end up missing by?" This way you are not questioning her call, but you're making her think about it and mentally review where she saw the ball land. If she's not able to give a clear response, then maybe you need to sit down and have a chat sometime. But if she replies with confidence without having to think about it too much, then she's probably calling it right.