My card is over charged

Did you accidentally paid twice? or was it because of the pre-authorized payment setup?

I remember paying it once, i didn't add amount 2 times for card transaction. Will they refund the amount? 

I do not believe so. However, a credit should show up on your account for the second payment, so you do not need to pay for the next month.

If you only paid once and as the status of the credit payment was still “processing”, I suggest you wait until it is “processed”/“authorized”. There could be issues with the credit card system also.