It's not wrong to apply separately. Many a times married couples also apply independently due to circumstances. So it's not something that's not allowed.
Why don't you calculate your crs score independently and see how each of you is placed? If you both have good crs scores (445 and above is a safe score currently) then there's no risk at all.
But if one of you is weak in English (unable to get a good IELTS score) or doesn't have enough work experience or a high education to get the required crs score then it would be risky to do it separately. If this is the case, try and arrange for a concrete proof of your common law relationship and apply together.