To reproduce, run setup(), then run reindex() and count() in parallel:

var n = 1000

function setup() {
    db.c.drop()
    for (var i=0; i<n; i++)
        db.c.insert({_id:i, x:i})
    db.getLastError()
}

function reindex() {
    for (;;) {
        db.c.reIndex()
        sleep(1)
    }
}

function count() {
    for (;;) {
        var nn = db.c.find().hint({_id:1}).batchSize(n).itcount()
        if (n != nn)
            print('expected', n, 'got', nn)
    }
}

• As written above, with a large enough batchsize to avoid getmore, when the query yields it finishes without error and returns only a subset of the documents (which is always one less than a multiple of 128, the unit of work for yielding). If the query is not able to return full results it should return an error.
• If the code is modified to use a small batch size so that getmores occurs, the query errors out with a CursorNotFound, which is acceptable.