There are 2 problems that happen. Firstly 2FA that is mandatory now in India is not properly supported by US cards. VBV/MSC needs to be enabled on your cards. Secondly, you can also let your bank know that you're doing a transaction on the Indigo website and that they should let that transaction through. US Amex usually works the best, they support 2FA by default.

Or book through an OTA.