I found that when i use arduino Uno board for this application (motor speed reading), I get error at around 20000 counts/sec (105rpm).
When i use arduino MKR1010 wifi board for same application, I get error at around 35000 counts/seconds (250rpm).
when i use arduino Due board for same application, I did Not get any error even beyond 1,00,000 counts/secons (800rpm).
SO, my understanding says that this is because of the processing speed/clock speed/speed of external interrupt pins of my arduino.
So, if you have similar problem, try arduino Due, which has 84MHz clock speed (V. good). But, still I don't know the exact answer. Looking for more precise answer.
Hope this will be useful for others.