The chances of receiving a tax assessment or request for additional info are quite high over the course of a small business' existence. It is even more likely in Quebec given that most people have to file two tax returns.
Tax assessments are often difficult to understand (surprisingly the explanations can be insufficient and/or confusing). If you had an accountant file your tax return, it is a good idea to consult them upon receipt of an assessment. If you filed it yourself, and do not understand the assessment, you should call the government agency. They are usually eager to help, if not always illuminating. If you still do not understand it or feel that there has been a misunderstanding, it is probably best to contact an accountant.
If you do not agree with assessment, and are comfortable with the reasons, you can file a notice of objection.
Both the federal and Quebec revenue agencies require that you maintain tax documentation for 7 years. It is always helpful and less stressful to have well organized, easily accessible documentation since unfortunately our memories are notoriously unreliable.
In some cases interest and penalties are charged for late filing. If the late filing was a result of extenuating circumstances or government error, one can apply for a waiver using forms available at Revenue Canada or Revenue Quebec.
It is imperative to deal with a tax assessment as soon as possible. If you are not in a position to respond to it quickly, you should at the very least contact the CRA or RQ and ask for an extension. The government does makes mistakes, and often deductions and credits are a matter of interpretation.