1. Sec 44AD talks about presumptive taxation. It is available only to the eligible assessee. Make sure in your case the assessee is an eligible assessee.
2. Sec 44AD is not applicable by default. It is an option available to the assessee. Eligible assessee having a T.O of less than Rs. 2 crores during the year can opt for this section and pay tax at 8% or 6%.
3. If the T.O is less than Rs. 1 crore then audit u/s 44AB will not be applicable. Criteria for determining the audit u/s 44AB is T.O and not profit or loss.
4. In your case, if the assessee is carrying on business tax audit u/s 44AB will not be applicable as his T.O is less than Rs. 1 crore. Make sure he is not covered u/s 44AD(4).
Please correct me if the above solution has an alternative view.