SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    65531, 65463, 65701, 65298, 65563, 65698, 
    65461, 65426, 65299, 65521, 65560, 
    65796
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00130

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "9",
      "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
      "rowid_filter": {
        "range": {
          "key": "lower_limit",
          "used_key_parts": ["lower_limit", "product_id", "usergroup_id"]
        },
        "rows": 24,
        "selectivity_pct": 0.889547813
      },
      "rows": 24,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (65531,65463,65701,65298,65563,65698,65461,65426,65299,65521,65560,65796) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result