Your payroll department are wrong. There are more details here:
http://www.hmcourts-s...ice/faq_employers.pdf
Your employer is supposed to process your payroll as normal and then simply not pay you the appropriate net amount. That way your tax and ni is correctly paid over. The travel expenses should certainly have no relevance here (it's not entirely clear from your first sentence if the £414.85 includes travel expenses or was paid in addition to them).
Is it worth worrying about? Probably not. Technically you haven't paid enough tax (or NI) but there's not a chance of anyone noticing it and even if the Revenue were aware it would hardly be worth their while bothering with it for the £30 or so you've gained on the deal.