IT ACT on residence cum office concept

Being account I am in dilemma as Auditor does not speak out.

We are having 18 cos on single floor [ no idea about geo tagging under MCA].. Particularly father owns Pvt Ltd Co and 3 sons are having respective LLP but father unit has leased plant to all.

They live in a 6 storied flat but treat residence as office cum residence [ actually untrue] and all construction and repair costs are borne by LLP.

Is it correct as pet Income Tax Act?  

Kindly guide accountant how to deal with?