Tax deduction on purchase of software

Dear Sir's and Friends, Our company has purchased a software from US Based company. We have made payments to this company without deducting Withholding Tax. My question is that as per Section 9 any payments made cross border for FTS & Royalty is taxable not considering the Permanent Establishment and Business Connection Factor. In short any payment made for FTS and Royalty subjects to deduction of Witholding Tax. I do not understand how our senior people have allowed this and since it is Software purchased how will it be disallowed as the same is not w/off in P&L. Please advise