I was off for 3 day with a Dr's note stating I couldn't work. My employer told me that those days were used against my vacation days. Is that right?

This depends on what Province you are employed in. For example, Ontario provides for three unpaid sick days, while British Columbia provides five paid sick days. Your employer cannot force you to use vacation days to cover sick days, but depending on your Province of employment this may result in you not being paid for days when you are sick.