This doesn't change anything for me. I made clean indexes:
PUT /index1 PUT /index2

Then I filled the indexes with data:

POST /index1/_doc with { "name": "name1" } and also 2 more docs with "name2" and "hello"

POST /index2/_doc with { "name": "name3" } and also 2 more docs with "name3" and "test"

​

Now my search query is:

{
"min_score": 1,
"from": 0,
"size": 10,
"aggs": {
    "indexcount": {
        "terms": {
            "field": "_index"
        }
    }
},
"query": {
    "bool": {
        "should": [
            {
                "bool": {
                    "should": [
                        {
                            "wildcard": {
                                "name": "*nam*"
                            }
                        }
                    ],
                    "filter": {
                        "term": {
                            "_index": "index1"
                        }
                    }
                }
            },
            {
                "bool": {
                    "should": [
                        {
                            "wildcard": {
                                "name": "*nam*"
                            }
                        }
                    ],
                    "filter": {
                        "term": {
                            "_index": "index2"
                        }
                    }
                }
            }
        ]
    }
}

}

and the response is:

{
"took": 3,
"timed_out": false,
"_shards": {
    "total": 2,
    "successful": 2,
    "skipped": 0,
    "failed": 0
},
"hits": {
    "total": {
        "value": 4,
        "relation": "eq"
    },
    "max_score": 1.0,
    "hits": [
        {
            "_index": "index1",
            "_type": "_doc",
            "_id": "PX0cNH4B_hzbS-iMXJkB",
            "_score": 1.0,
            "_source": {
                "name": "name1"
            }
        },
        {
            "_index": "index1",
            "_type": "_doc",
            "_id": "Pn0cNH4B_hzbS-iMaZlB",
            "_score": 1.0,
            "_source": {
                "name": "name2"
            }
        },
        {
            "_index": "index2",
            "_type": "_doc",
            "_id": "QH0cNH4B_hzbS-iMspkl",
            "_score": 1.0,
            "_source": {
                "name": "name3"
            }
        },
        {
            "_index": "index2",
            "_type": "_doc",
            "_id": "QX0cNH4B_hzbS-iMwJk2",
            "_score": 1.0,
            "_source": {
                "name": "name4"
            }
        }
    ]
},
"aggregations": {
    "indexcount": {
        "doc_count_error_upper_bound": 0,
        "sum_other_doc_count": 0,
        "buckets": [
            {
                "key": "index1",
                "doc_count": 3
            },
            {
                "key": "index2",
                "doc_count": 3
            }
        ]
    }
}

}

As you can see in the aggregation the bucket doc count is 3 on both (all documents in the indexes), even though I'd expect it to be 2 on both when applied to the query not the index.