How to remove blockages in MongoDB when multiple write query comes for same collection at same time
From the database perspective you can try using, MongoDB 3.0 with the Wired Tiger storage engine to eliminate these waits. MongoDB 3.0 with the Wired Tiger uses Document level blocking and thus brings down the waits considerably.

In case this is not possible, then you cannot do much on the database layer and will either need to live with these waits or will need to handle it from the Application layer.

A tentative approach, which can be used to  provide control of the waits from the Application layer can be to queue the respective transactions in the application so that the user does not need to make the changes multiple times.