SELECT 
  DISTINCT(
    cscart_product_bundle_product_links.bundle_id
  ), 
  linked_promotion_id 
FROM 
  cscart_product_bundle_product_links 
  LEFT JOIN cscart_product_bundles ON cscart_product_bundles.bundle_id = cscart_product_bundle_product_links.bundle_id 
WHERE 
  product_id IN (241) 
  AND linked_promotion_id IN (26, 27, 25)

Query time 0.00041

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "2.40"
    },
    "duplicates_removal": {
      "using_temporary_table": true,
      "using_filesort": false,
      "nested_loop": [
        {
          "table": {
            "table_name": "cscart_product_bundle_product_links",
            "access_type": "ref",
            "possible_keys": [
              "PRIMARY",
              "bundle_id"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "using_index": true,
            "cost_info": {
              "read_cost": "1.00",
              "eval_cost": "0.20",
              "prefix_cost": "1.20",
              "data_read_per_join": "24"
            },
            "used_columns": [
              "bundle_id",
              "product_id"
            ]
          }
        },
        {
          "table": {
            "table_name": "cscart_product_bundles",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "bundle_id"
            ],
            "key_length": "4",
            "ref": [
              "satishecarter_march_003.cscart_product_bundle_product_links.bundle_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 0,
            "filtered": "50.00",
            "cost_info": {
              "read_cost": "1.00",
              "eval_cost": "0.10",
              "prefix_cost": "2.40",
              "data_read_per_join": "20"
            },
            "used_columns": [
              "bundle_id",
              "linked_promotion_id"
            ],
            "attached_condition": "(`satishecarter_march_003`.`cscart_product_bundles`.`linked_promotion_id` in (26,27,25))"
          }
        }
      ]
    }
  }
}