This is commonly due to a mix up when performing the merge. If customer (or vehicle) A is merged into B, the database entry for B will now contain all information common to A and B and the entry for A will be deleted.
The mix up could occur if you are not careful when assigning the customers (or vehicles) to merge.
This is similar for vehicles. Please make sure that you have allocated the customers (or vehicles) correctly into the fields.
Barring this, if the problem persists, please contact the MechanicDesk Support Team.