And since you've already been going through the missionary accounts, it might be helpful to also try and determine how the missionary funds got to that point for this missionary. Each situation is unique, but sometimes there are patterns that either can help out with other missionaries currently serving, or perhaps specifically when the same family has their next missionary leave as is your case.
For instance, sometimes families pre-pay (even though that's strongly discouraged), and others continue to donate on their own which effectively multiplies what accumulates in the account. Other times, there's no tracking of who is donating, and various family and ward members are making individual donations that have a cumulative effect of overpaying. And sometimes families actually understand the process and are expecting to apply the overage to their next missionary, but maybe not everyone is aware of this.
In any case, it would also be good to determine if this was something that the ward could have identified a number of months ago, and taken action to help avoid the 3 month overage. And then add that into what you are tracking at regular intervals for missionary fund balances.