when we calculate the total ATP formed in aerobic respiration, it comes out to be 38. But our teacher said that the net gain is 36 ATP. Where did the 2 molecules are utilised?

Yes,total gain of  ATP under standard conditions is considered to be 38 from aerobic respiration of one molecule of glucose( In reality 30-32 ATPs formed). Formation of 38 or 36 ATP from aerobic respiration of one glucose molecule depends on whether the malate shuttle or the glyceraldehyde shuttle is being used for transferring  cytoplasmic NADH to mitochondrion to undergo oxidative phosphorylation process. As 36 is more near to reality number of ATP formation , then this is considerd more accurate than 38 ATP.