Mere disallowance of expenses itself is not a suffecient ground to levy penalty u/s 271.1.c.
As part of expenses ahve beenallowed by the CIT(A), the matter is contentious on which difference of opinion exists. So penalty is not leviable.
The nature of expenses and evidence should be to establsih pramafacie allowability of the case.If similar expenses have been allowed fully in past (even in order u/s 143.1, the claim is established and a disallowance cannot be ground for penalty.
Even a bonafide mistake can be a ground not to impose penalty - see cases of Reliance Petrolium and PWC.
Even after amendment of s.271.1.c and some judgments of SC holdign that amendment is retrospective,and penalty can be levied in case of loss, the merits of claim and arguablable status will absolve from levy of penalty.
It would be better to file appeal against order of CIT(A) to seek further relief. In case revenue has filed an appeal, then assessee can file appeal by way of Cross Objections without any fees for ITAT.
Eligible B/f losses have to be set off, there is no legal option not to set off losses except in case of some capital gains.