Apparently, the collapse query selects one of the documents in the group as a leader and selects it for counting facets, and in one of the group, the leader which was getting selected didn't have the field considered for facets.
Solr count mismatch between facet and filter query
Apparently, the collapse query selects one of the documents in the group as a leader and selects it for counting facets, and in one of the group, the leader which was getting selected didn't have the field considered for facets.