Code to reproduce https://jira.mongodb.org/browse/SERVER-1285

collection-stats.js

db.collection.stats()
{
	"sharded" : true,
	"flags" : 1,
	"ns" : "database.collection",
	"count" : 42821370,
	"numExtents" : 80,
	"size" : 38573270908,
	"storageSize" : 43791466336,
	"totalIndexSize" : 2008426224,
	"indexSizes" : {
		"_id_" : 2008426224
	},
	"avgObjSize" : 900.7948813407885,
	"nindexes" : 1,
	"nchunks" : 945,
	"shards" : {
		"rs1" : {
			"ns" : "database.collection",
			"count" : 20662481,
			"size" : 20199884736,
			"avgObjSize" : 977.6117754687832,
			"storageSize" : 24042160032,
			"numExtents" : 41,
			"nindexes" : 1,
			"lastExtentSize" : 2146426864,
			"paddingFactor" : 1.009999999955934,
			"flags" : 1,
			"totalIndexSize" : 977416272,
			"indexSizes" : {
				"_id_" : 977416272
			},
			"ok" : 1
		},
		"rs2" : {
			"ns" : "database.collection",
			"count" : 22158889,
			"size" : 18373386172,
			"avgObjSize" : 829.1654952556511,
			"storageSize" : 19749306304,
			"numExtents" : 39,
			"nindexes" : 1,
			"lastExtentSize" : 2146426864,
			"paddingFactor" : 1.0099999999444642,
			"flags" : 1,
			"totalIndexSize" : 1031009952,
			"indexSizes" : {
				"_id_" : 1031009952
			},
			"ok" : 1
		}
	},
	"ok" : 1
}

MultipleIDQueryTest.java

import java.util.ArrayList;
import java.util.List;

import com.mongodb.BasicDBObject;
import com.mongodb.DBCollection;
import com.mongodb.DBCursor;
import com.mongodb.DBObject;
import com.mongodb.Mongo;


public class MultipleIDQueryTest {

	private static final String MONGO_URL   = "localhost";
	private static final String DATABASE    = "database";
	private static final String COLLECTION  = "collection";
	private static final int    MAX_NUM_IDS = 10000;

	public static void main( String[] args ) throws Exception {
		Mongo mongo = new Mongo(MONGO_URL);
		try {
			DBCollection collection = mongo.getDB(DATABASE).getCollection(COLLECTION);
			long collectionSize = collection.count();
			if ( collectionSize < MAX_NUM_IDS ) {
				throw new RuntimeException("collection has too few ids: " + collectionSize);
			}

			List<Object> ids = collectSomeIds(collection);

			for ( int queryLimit = 500; queryLimit <= MAX_NUM_IDS; queryLimit += 500 ) {
				BasicDBObject query = new BasicDBObject("_id", new BasicDBObject("$in", ids.subList(0, queryLimit)));
				DBCursor cursor = collection.find(query).limit(queryLimit);
				int itCount = 0;
				while ( cursor.hasNext() ) {
					cursor.next();
					itCount++;
				}
				int cursorCount = cursor.count();
				System.out.printf("cursor.count(): %5d | itcount: %5d  ", cursorCount, itCount);
				if ( itCount != cursorCount || itCount != queryLimit ) {
					System.out.println("FAIL!");
				} else {
					System.out.println("OK");
				}
			}
		}
		finally {
			mongo.close();
		}
	}

	private static List<Object> collectSomeIds( DBCollection collection ) {
		List<Object> ids = new ArrayList<Object>();
		for ( DBObject o : collection.find() ) {
			ids.add(o.get("_id"));
			if ( ids.size() >= MAX_NUM_IDS ) break;
		}
		return ids;
	}
}

output.log

cursor.count():   500 | itcount:   500  OK
cursor.count():  1000 | itcount:  1000  OK
cursor.count():  1500 | itcount:  1500  OK
cursor.count():  2000 | itcount:  2000  OK
cursor.count():  2500 | itcount:  1445  FAIL!
cursor.count():  3000 | itcount:  3000  OK
cursor.count():  3500 | itcount:  3500  OK
cursor.count():  4000 | itcount:  4000  OK
cursor.count():  4500 | itcount:  4500  OK
cursor.count():  5000 | itcount:  5000  OK
cursor.count():  5500 | itcount:  5500  OK
cursor.count():  6000 | itcount:  6000  OK
cursor.count():  6500 | itcount:  6500  OK
cursor.count():  7000 | itcount:  7000  OK
cursor.count():  7500 | itcount:  7500  OK
cursor.count():  8000 | itcount:  7483  FAIL!
cursor.count():  8500 | itcount:  6572  FAIL!
cursor.count():  9000 | itcount:  6072  FAIL!
cursor.count():  9500 | itcount:  5572  FAIL!
cursor.count(): 10000 | itcount:  5564  FAIL!