What happens when a contractor finishes work but on inspection it needs some repairs,do i expense the entire invoice amount?

Here expenditure book by the percentage of work & also make payable into same amount.

whenever we made payment (running payment or partial payment) to contractor we deduct some percentage of amount called Retention is safe for us

Finally any repairs we use that money to concern expenses then we will pay the final net amount to Contractor

No .. if contract says  he can receive for the finished stage you can  up to completed work stage after the inspection . Or else you can pay full invoice amount after the work is completed fully.

we can pay the contractor a part of the invoice and make an agreement with him to pay the other part after the inspection

No we convince with the contractor request the base of future contract to complete this as compliment