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 (
    65688, 65103, 65454, 65694, 65102, 65596, 
    65696, 65519, 65597, 65683, 65613, 
    65702, 65608, 65716, 65717, 65697, 
    65695, 65690, 65568, 65612, 65602, 
    65610, 65851, 65611
  ) 
  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 0.00123

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": 48,
        "selectivity_pct": 1.779095626
      },
      "rows": 48,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (65688,65103,65454,65694,65102,65596,65696,65519,65597,65683,65613,65702,65608,65716,65717,65697,65695,65690,65568,65612,65602,65610,65851,65611) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result