Hi Amit,
There is no need to worry, if the payment has been deducted from your PayTm wallet and it is not reflecting back on the portal, Just take the screenshot of that transaction from PayTm application and drop an email on ugadmission@vit.ac.in and share your query with them and you can expect a reply within 24-48 hours. Also the last date to fill the form is extended, so don't worry.
Feel free to contact if any further issue arises.