[{"github_open_issues":{"0":{"git_url":"https://github.com/","git_assignees":"None","git_open_date":"2019-09-26","git_id":253113,"repo":"repoA","git_user":"userA","state":"open"},"1":{"git_url":"https://github.com/","git_assignees":"None","git_open_date":"2019-11-15","git_id":294398,"repo":"repoB","git_user":"userB","state":"open"},"2":{"git_url":"https://github.com/","git_assignees":"None","git_open_date":"2021-04-12","git_id":661208,"repo":"repoA","state":"open"}},"unique_label_seen":{"568":{"label_name":"some label","times_seen":12,"535":{"label_name":"another label","times_seen":1}}}}]

db.collection.aggregate([{$addFields:{github_open_issues:{$filter:{input:{$objectToArray:"$github_open_issues"},cond:{$in:["$$this.v.repo",["repoA"]]}}}}},{$match:{github_open_issues:{$ne:[]}}},{$addFields:{github_open_issues:{$arrayToObject:"$github_open_issues"}}}])