Having one visitor visa application rejected is not negative in itself. It shows that couples want to share their lives together.
What can/will pose a problem for you is that your wife didn't mention this visitor visa rejection in the application. There is a question in th forms that specifically asks if there has ever been a visa denied to Canada or other countries. So the fact that your wife didn't answer this is a lie and misrepresenting herself. It doesn't matter if you weren't married at the time. It was asking about her visa application history. Now, that being said, because this visitor visa rejection was for Canada, and the vo will be able to see the application history to Canada, maybe it won't be a big deal. But if I were you, and sponsor approval has already happened, I would use the uci number and send an updated form to the visa office abroad and rectify this information telling the truth and explaining that a visitor visa to Canada was denied.