you will need to explain as to why you failed to register for studies in time and obviously your study permit will expire before your course finishes and then you'll have to explain the same at the time of study permit extension. It will also affecct your spouse's case as I really doubt CHC will let your spouse into Canada if you're not registered and studying (which is primarily you're there for !!!). I'd suggest you to hire a good immigratio lawyer when you file your spouse's application.
Cheers ;-)