It sounds more like a lack of familiarity with the program than a glitch.
Without knowing exactly what you filled in where, I would have recommended doing one of the following:
1. Checking your bottom line summary under the review tab would have shown the error, and double-clicking the line would have suggested auto expense, office in home costs and capital cost allowance.
2. If you had clicked on the income tab, you would have seen a section for employment expenses, which might have helped you locate it.
3. Start a new return from scratch. It's the fastest way to deal with this situation when you are not familiar with the software.
Hopefully CRA gets you sorted out soon.
