CIC cares about the Highest Degree.
What I have observed on this forum is that for many people, WES has evaluated their Masters degree to be a Canadian Bachelor's equivalency. Specially from Asian countries. So if you just send your Masters degree, and WES evaluate it to be a Bachelors, you will get points for 1 Bachelor degree only. Whereas, if you send your Bachelors degree too, you will have points for 2 degrees of more.
Also, In India, some of the Bachelors degrees are a 3 years course. If you have a Masters degree after a 3 years Bachelors degree, in that case WES specifically asks to send both the degrees.