I would advise husband to wait another 1-2 weeks to cover possible miscalculations of physical presence (for instance one of the stamps in my passport made CBSA was one day before I crossed the border, while in their records they had correct day). If i had applied based on stamps in passport right after 1,095 days of presence in Canada, I would have been one day short of required period.
Also there is extremely high risk that your spouse will get RQ and eventually (after couple years) her application will be rejected. That's just my opinion.