It is not uncommon for most people to just receive their notice of assessment after filing their taxes and just accepting them as being totally accurate. The figures may be different than what you submitted concerning the tax return, but you just assume that the tax people are right and you are wrong.
Any government body can make a mistake and the CRA is not exempt from this. This is why they have recourses in place when you do not agree with their findings. The other thing is tax law is a matter of interpretation, and sometimes with complex tax matters it means that the applicable laws have to be scrutinized and ruled upon.
In general with the average tax return and changes in the assessment it often comes down to the tax preparer making an error. It could be a math error, or not understanding the tax form properly.
It really is important to compare your assessment with your actual tax return to see where any discrepancies are. If you feel that the assessment is not right then you can file a notice of objection.
If you are using the online services with CRA you can log into your account and go to the option for registering a formal dispute. If it is business related go to your business account that you have registered with the CRA and select the registering a formal dispute, notice of objection.
If you are not using online services you can write directly to the Chief of Appeals explaining your dispute or you can fill out Form T400A, Objection. Be absolutely sure to explain in detail what you are objecting to, and provide copies of any supporting documentation related to this.
Normally you only have 90 days to do this, but there are exceptions.
If you have used accounting services, be sure to bring this matter to the attention of the professional who completed your return for you. They will either explain why the tax department is right, or help you with your objection. Even if you lose your objection you can still go a step further with an appeal.
Many people are intimidated by the CRA and feel that they should never challenge them. In the past perhaps this government body as helped to create this type of negative approach. Recently they have been working at promoting their image as being there to help the tax payer.
Taxes are set by law and you are entitled to challenge those responsible for enforcing these if you believe they are doing so in error. If you have approached your tax responsibilities in the proper manner you should not fear contact with the CRA.