No extra fees are not paid by the AICTE, it only pays the amount which was already discussed earlier. Some colleges do not demand the extra academic fees but few colleges also demand them, If the college fees are more than 1.25 lakhs then the student may have to pay the left amount from the maintenance charges paid to the student by AICTE.
It is the responsibility of the student to know about the college fees structure before filling the college in the choice filling. If your college is in Maharashtra then don't worry you will not be charged extra as the govt there has mentioned that no college will demand extra academic fees from the AICTE students.
You can check a similar answer from this linki below.
do i have to pay the extra fee if the college fee is more than the scholarship given by aicte?