I've got a collection called payments with an example of its document shown below:
{
    "_id" : ObjectId("579b5ee817e3aaac2f0aebc1"),
    "updatedAt" : ISODate("2016-07-29T11:04:01.209-03:00"),
    "createdAt" : ISODate("2016-07-29T10:49:28.113-03:00"),
    "createdBy" : ObjectId("5763f56010cd7b03008147d4"),
    "contract" : ObjectId("578cb907f1575f0300d84d09"),
    "recurrence" : [ 
        {
            "when" : ISODate("2016-05-29T11:03:45.606-03:00"),
            "_id" : ObjectId("579b6241ea945e3631f64e2d"),
            "transaction" : {
                "createdAt" : ISODate("2016-05-29T11:03:45.608-03:00"),
                "tid" : "9999999999999999B01A",
                "status" : 4,
                "code" : "00",
                "message" : "Transação autorizada"
            },
            "status" : "PAGO"
        }, 
        {
            "when" : ISODate("2016-06-29T11:03:45.608-03:00"),
            "_id" : ObjectId("579b6241ea945e3631f64e2c"),
            "transaction" : {
                "createdAt" : ISODate("2016-06-29T11:03:45.608-03:00"),
                "tid" : "9999999999999999B01A",
                "status" : 4,
                "code" : "00",
                "message" : "Transação autorizada"
            },
            "status" : "PAGO"
        }, 
        {
            "when" : ISODate("2016-07-29T11:03:45.608-03:00"),
            "_id" : ObjectId("579b6241ea945e3631f64e2b"),
            "status" : "ERRO",
            "transaction" : {
                "code" : "56",
                "createdAt" : ISODate("2016-07-29T11:04:01.196-03:00"),
                "message" : "Autorização negada",
                "status" : 5,
                "tid" : "1006993069000730B88A"
            }
        }, 
        {
            "when" : ISODate("2016-07-30T11:03:45.608-03:00"),
            "_id" : ObjectId("579b6241ea945e3631f64e2a"),
            "status" : "PENDENTE"
        }, 
        {
            "when" : ISODate("2016-07-31T11:03:45.608-03:00"),
            "_id" : ObjectId("579b6241ea945e3631f64e29"),
            "status" : "PENDENTE"
        }, 
        {
            "when" : ISODate("2016-08-01T11:03:45.608-03:00"),
            "_id" : ObjectId("579b6241ea945e3631f64e28"),
            "status" : "PENDENTE"
        }
    ],
    "status" : "PAGO",
    "conditions" : {
        "originalValue" : 7406.64,
        "totalValue" : 7400,
        "upfrontValue" : 1500,
        "upfrontInstallments" : 3,
        "balanceInstallments" : 9
    },
    "__v" : 0,
    "transaction" : {
        "code" : "00",
        "createdAt" : ISODate("2016-07-29T10:49:46.610-03:00"),
        "message" : "Transação autorizada",
        "status" : 6,
        "tid" : "1006993069000730AF5A"
    }
}
If I run the query below, I get the desired document shown above:
db.payments.find({ "recurrence.transaction.tid": "1006993069000730B88A" })
However, if I run this other query, MongoDB returns my entire collection (presumably because it didn't match the subdocument's id):
db.payments.find({ "recurrence._id": ObjectId("579b6241ea945e3631f64e2b") })
Both queries should return the same result! I also checked some other questions including this one so unless I'm going crazy I'm doing the same thing. Not sure why the inconsistent results though.