There's nothing 'offensive' about the expression "good job". It isn't particularly informal but it isn't overly formal either. Opinions may vary, but we don't give opinion-based answers on this site.
Some people are what you might call 'hypercritical' - constantly looking for fault, quick to assume the worst about others. If you have a boss like that then I suppose it is possible he might find the language a little formal. Some people in business expect 'corporate speak' (an excessively formal, cliche-ridden, responsibility-avoiding form of language that sadly has become the norm in some businesses). In such an environment, you might have instead written "I trust that we have now satisfactorily completed the task to specification, but please advise me if there is anything further I can do"... but really, I wouldn't worry, you won't have 'offended' anyone.