Original return processed and not revised

My cousin was trying to file his return on 15th. He is in the non taxable slab. The website was not working well. So, he filed with whatever the prefilled data showed. He had a refund of around Rs. 500/- from tds. Yesterday he filed the revised return under section 139(5) and added his US stock data under the relevant schedules as per his brokers report and some Indian capital gain data. The refund again in this return was the same Rs. 500/- Today he received the intimation and the got the refund in his bank but when he checked he found that they have processed the original return instead of the revised one. Weren’t they supposed to process the revised return? I thought the original return is null and void once the revised return is filed. What to do in this case now?