How deep they go depends on what they suspect you're doing that's wrong. Their computers are very good at raising red flags. If you live and work on a farm, but still claim the transit credit...well you guess what's going to happen. If you have many other irregularities they're only going to dig deeper.I've had a few minor adjustments made when my T3 or T5 slips are late and I don't bother to make the adjustments afterwards. It almost always gets caught. Now I have the slips generated electronically through my discount broker and it won't be a problem in the future....other than that no other issues, but I too would like to hear about some of the auditor tactics and the scope of there investigations and how deep they go in an audit.
I was audited 4 years in a row during my college years. My (single) mother maximized some of the tuition tax credits by declaring me a spousal equivalent and earned rather large returns (she had a high income). This kept setting off a red flag, as I guess it's a common fraud tactic for high earners. :-/
The CRA is actually quite reasonable (taking our money away from us aside . My mom and I just mailed in the forms and that was it. On the 4th audit, we told them that it's unreasonable how we kept getting flagged and the woman on the phone agreed and cancelled the audit and we never got another one. All they want is proof, so if you're going to claim make sure you can back it up.