I'm using an unique index:

    {
        "v" : 1,
        "unique" : true,
        "key" : {
            "state.agent" : 1
        },
        "name" : "state.agent_1",
        "ns" : "live.tasks.active",
        "partialFilterExpression" : {
            "state.value" : "assigned"
        },
        "background" : true
    }

My applications works in a way that many times an update (using $set and $unset) is sent that should be rejected with an ""E11000 duplicate key error collection: live.tasks.active index: state.agent_1" because of duplicate value in the above index.
After running for ~20 days I realized that above index has become inconsistent with collection data in a way that a query using _id show's a document that should be in this index:

db.tasks.active.find({_id:ObjectId("57bea0f21ebfd0b31f32da1c")})

but a query that shows all data in the index doesn't show that document:

db.tasks.active.find({"state.value":"assigned"}, {"state.agent": 1})

I have tried to do a db.tasks.active.reIndex(), but it failed with a message that db.tasks.active contains duplicate values for an above index so that above index cannot be re-added.
It seems that because of an error sometimes a duplicate index value is allowed to enter into a collection document instead of returing ""E11000 duplicate key error collection: live.tasks.active index: state.agent_1".
I suspect that after this an index becomes inconsistent: isn't updated everytime as it should.

Most times I do get E11000, but from time to time update doesn't return an error (as it should) and updates a document making a duplicate index key entry that is not visible in the index itself.