There are a few ways to 'silent' the incoming call. One is by pressing the volume rocker or the power button, which is probably what happens most often if inside your bag.
Also, if the motion setting is on and the phone is in your bag and it's moving around too much, it MAY trigger the silencing by thinking you turned the phone down. Remember that it uses both the motion sensors and the proximity sensors, and if you're using the flip cover (which doesn't latch close) the flapping, even if slight, can cause the phone to sense that the IR sensor was unblocked and is now blocked. I know, for instance, that sometimes the 'wave your hand to answer' is triggered by this in rare occasions.