Yeah true if we look at the RFID module level then the code I'm working out doesn't make much sense but the code I'm working right now is one of the important block for that project and I didn't mention much about the project since the beginning because it will mislead the topic.
Anyways, thanks for the help so far, I was able to read data reliably till 32us time period, my aim is to read even the 16us time period signals without even those small errors. I will try to implement the same code in Atmel studio directly with port manipulation to compensate the error further. Also instead of using digitalRead(), I will directly use the (PINX & (1<<PBX)) function and ISR in Atmel studio, hopefully, it might work much efficiently.
Thanks guys. 