The following example is based on the in6.js test:

t = db.jstests_in6;
t.drop();

t.save(

);
t.save(

);
t.save(

);
t.save(

);
t.save( {} );

function doTest() {
assert.eq.automsg( "1", "t.count(

)" );
assert.eq.automsg( "1", "t.count( {key:{$in:[[]]}} )" );
}

doTest();
t.ensureIndex(

);
doTest();

The first query using

works as expected as long as there is no index (seems to be the same as http://jira.mongodb.org/browse/SERVER-1943), but the second query {key:{$in:[[]]}} returns nothing in both cases.