My refund from CRA is significantly less than from TurboTax ($46.22 vs $825.22). What caused this?

This wasn't an issue if it weren't for the fact that this year, I had to file taxes with my wife separately and I had to pay $654.77 for my wife's tax return. We just have a T4 and T5s, no special situations, and this just doesn't make sense to me.