Hi Tejas,
Yes, I have seen this problem before, in particular, when using API version > 2015-09-08. When listing charges via /v1/charges some card charges may not be listed, and I suspect that's because of a bug in the implementation in 2015-09-23 that aggregates both card and bank charges ("charges now returns all charges, such as card charges and bank account charges"). I had to resort to downgrading my tool to use API version
2015-09-08, the latest version that doesn't have this problem (I used identical GET requests, with the only difference being the API version specified in the Stripe-Version request header).
I've been meaning to log a bug with Stripe, but have been pre-occupied with other urgent matters so far.
Hth,
Jeffri