Only received around half of the estimated amount that turbotax had told me. In the years I've done this nothing like this has ever happened?

While it can be frustrating, it’s common for the Canada Revenue Agency (CRA) to make a tax return assessment that is different from yours. 

The reasons for these discrepancies may vary, and can range from very simple (typo or data entry error, forgotten slip, receipt, amount, etc) to complex (carry-forward amounts not included, accounting errors, etc).

In most cases, the CRA will explain how they calculated your tax refund or balance owing, and you can find this information on your Notice of Assessment (NOA), under the heading Explanation of changes and other important information. Compare the line numbers on your NOA and their corresponding values with those entered into TurboTax.