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 (
    2825, 2303, 2302, 2562, 2563, 2564, 11788, 
    2343, 11790, 12698, 2268, 2269, 2316, 
    4395, 2315, 2626, 2624, 11804, 11803, 
    2842, 2741, 12711, 12697, 11802, 2255, 
    2256, 2383, 2380, 12657, 2321
  ) 
  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 0.00791

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": 6.888854504,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (2825,2303,2302,2562,2563,2564,11788,2343,11790,12698,2268,2269,2316,4395,2315,2626,2624,11804,11803,2842,2741,12711,12697,11802,2255,2256,2383,2380,12657,2321) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}