> use mongo_bug
> db.bug_collection.ensureIndex({"nested.key2": 1}, {sparse: true})
> db.bug_collection.insert({key: 'a'})
> db.bug_collection.insert({key: 'b'})
> db.bug_collection.insert({key: 'c'})
> db.bug_collection.find({})
{ "_id" : ObjectId("4f0e7daf9be3426d0ba2e7b8"), "key" : "a" }
{ "_id" : ObjectId("4f0e7db59be3426d0ba2e7b9"), "key" : "b" }
{ "_id" : ObjectId("4f0e7dba9be3426d0ba2e7ba"), "key" : "c" }
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}, "nested.key2": {$ne: 'd'}})
# No results returned (expected, because of the sparse index?)
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}})
# No results returned (NOT expected)
> db.bug_collection.dropIndex("nested.key2_1") { "nIndexesWas" : 2, "ok" : 1 }
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}})
{ "_id" : ObjectId("4f0e7daf9be3426d0ba2e7b8"), "key" : "a" }
{ "_id" : ObjectId("4f0e7db59be3426d0ba2e7b9"), "key" : "b" }
{ "_id" : ObjectId("4f0e7dba9be3426d0ba2e7ba"), "key" : "c" }
#Query now works, after the index has been dropped.

The order of the queries also matters:

> db.bug_collection.dropIndex("nested.key2_1")
{ "nIndexesWas" : 2, "ok" : 1 }
> db.bug_collection.ensureIndex({"nested.key2": 1}, {sparse: true})
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}})
{ "_id" : ObjectId("4f0e811f89fc95d0a1a0356b"), "key" : "a" }
{ "_id" : ObjectId("4f0e812389fc95d0a1a0356c"), "key" : "b" }
{ "_id" : ObjectId("4f0e812589fc95d0a1a0356d"), "key" : "c" }
# Results returned (expected)
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}, "nested.key2": {$ne: 'd'}})
{ "_id" : ObjectId("4f0e811f89fc95d0a1a0356b"), "key" : "a" }
{ "_id" : ObjectId("4f0e812389fc95d0a1a0356c"), "key" : "b" }
{ "_id" : ObjectId("4f0e812589fc95d0a1a0356d"), "key" : "c" }
#Results returned (this same query returns nothing in first example)
> db.bug_collection.dropIndex("nested.key2_1") { "nIndexesWas" : 2, "ok" : 1 }
> db.bug_collection.ensureIndex({"nested.key2": 1}, {sparse: true})
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}, "nested.key2": {$ne: 'd'}})
# No results returned (as in first example)
> db.bug_collection.find({key: {$in: ['a', 'b', 'c']}})
# No results returned (as in first example)

It's as if the queries are considered equivalent and being cached.