Query on nested type with aggregation on nested types returns unexpected results - elasticsearch

Question

We are using elasticsearch 5.6.4. As mentioned in the ES documentation,
aggregation operates in the context of the query scope, any filter
applied to the query will also apply to the aggregation.
Now, what I have is this :
An index with mapping :
{
"properties":{
"asset":{
"properties":{
"customerId":{
"type":"long"
}
}
},
"software":{
"type": "nested",
"properties":{
"id":{
"type":"long"
},
"name":{
"type":"text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
}
}
}
I have created several documents to perform various tests here. Docs are indexed on customerId. I have in all 10 documents each having 2 or more softwares. For testing aggregations on softwares, I created softwares with same ID across multiple documents. e.g. I have software with Id as 12 twice in doc with customerId 1 and 2 and 3. Also, Doc with customerId 2 has two softwares with Id as 12.
So there are 4 softwares with Id as 12 across documents 1, 2 and 3.
The aggregation result includes only the documents with customerId 1 and not 2 and 3 ,when this query is run :
{
"query" : {
"term":{
"asset.customerId":1
}
},
"aggregations" : {
"aggs" : {
"nested" : {
"path" : "software"
},
"aggregations" : {
"software.id.agg" : {
"terms" : {
"field" : "software.id",
"size" : 10,
"min_doc_count" : 1,
"shard_min_doc_count" : 0,
"show_term_doc_count_error" : false,
"order" : [
{
"_count" : "desc"
},
{
"_term" : "asc"
}
]
}
}
}
}
}
}
But when the query filter is run on a nested type (software.id), aggregation result includes all the docs (1, 2 and 3) and hence the buckets which should be filtered out because of the query are also present. :
{
"query" : {
"nested" : {
"query" : {
"match_phrase_prefix" : {
"software.id" : {
"query" : 12,
"slop" : 100,
"max_expansions" : 50,
"boost" : 1.0
}
}
},
"path" : "software",
"ignore_unmapped" : false,
"score_mode" : "none",
"boost" : 1.0
}
},
"aggregations" : {
"aggs" : {
"nested" : {
"path" : "software"
},
"aggregations" : {
"software.id.agg" : {
"terms" : {
"field" : "software.id",
"size" : 10,
"min_doc_count" : 1,
"shard_min_doc_count" : 0,
"show_term_doc_count_error" : false,
"order" : [
{
"_count" : "desc"
},
{
"_term" : "asc"
}
]
}
}
}
}
}
}
What's the correct way to provide the query filter on nested type so that it is applied on aggregation?