my versions:

• elasticsearch 0.90.2
  plugins:
  -- mapper attachments 1.4.0
  -- river jdbc 2.2.1 (driver: postgresql-9.2-1002.jdbc4)
  -- elasticsearch-river-mongodb-1.6.11

Problem:
When I creating indexes for Postgre db everything works fine in head plugin for ES I see:
structure - name of index
size: 1mb (1mb)
docs: 3587 (3587)
But when i create index on mongo db I getting:
type - index name
size: 642.6kb (642.6kb)
docs: 10495 (10495)

But in docs field is wrong number of docs, because in my db I have only 3936 docs.
This problem exist on every index on mongo db - count of indexed docs not mach count of docs in db.

I'm creating indexes with ( it's a windows version):
curl -XPUT "http://localhost:9200/_river/body/_meta" -d "{ "type": "mongodb", "mongodb": { "servers": [{host: "localhost", port: "27017" }], "options": {"secondary_read_preference": true}, "credentials": [{db: "fis-bps",user: "guest", password: "guest"}], db: "fis-bps", collection: "body",gridfs: "false"}, index: {name: "body", throttle_size: 2000}}"

This problem only exist on Windows system. On Ubuntu system problem dosn't exist.

I noticed one more think: when I dump my DB, and remove all data for dbs (from data directory for primary and slave). I create databases, create index, and then restore database from dump.
Now i have correct count of indexed docs.

It looks like elasticsearch looks deep into mongo db and normal drop DB and recreate it, still leave some data which are used by elasticsearch to create indexes.