Rahul OMR sheets are thoroughly scanned and then with the help of the software it checks out the options which you have marked are correct or not and finally with the help of the software your total marks are calculated.

Now if you haven't marked the option circle properly with the pen then there can be a possibility that during scanning the machine might not accept your answer because of improper marking but if you have properly marked your answer's option with the pen and by mistake if some of it has gone out the bubble then it won't matter much and the scanning machine will accept your answer. 

Also soon most probably by 24th April JEE Main will release the answer key along with your scanned mark-sheet and if you find out any error in it then you can definitely notify JEE Mains administration.

Feel free to ask if you have any more queries. All the best!!