If you want to remove some query or query plan from query store, you can use the following commands:
EXEC sp_query_store_remove_query 4; EXEC sp_query_store_remove_plan 3;
Parameters for these stored procedures are query/plan id retrieved from system views.
You can also just remove execution statistics for particular plan without removing the plan from the store:
EXEC sp_query_store_reset_exec_stats 3;
Parameter provided to this procedure plan id.