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 (
    12669, 12975, 2299, 2297, 2298, 2203, 
    2566, 3215, 3214, 11118, 12685, 13990, 
    2340, 11888, 2339, 2338, 2180, 2181, 
    13661, 15141, 2228, 2226, 2227, 2336, 
    12743, 2185, 14298, 15154, 13222, 15155
  ) 
  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 0.00785

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "ref": ["const"],
          "rows": 6449,
          "filtered": 7.041940212,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (12669,12975,2299,2297,2298,2203,2566,3215,3214,11118,12685,13990,2340,11888,2339,2338,2180,2181,13661,15141,2228,2226,2227,2336,12743,2185,14298,15154,13222,15155) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}