It’s a lot easier to get inconsistent or bad cuts on non-Proofgrade materials. (Not necessarily trying to promote Proofgrade over anything else, they just engineer it to cut well.)
All I can suggest is to slow down the cuts a little…with any luck you’ll get through the knots and hidden glue plugs. Or maybe use a second pass. I’ve had trouble cutting through plywood and even Baltic Birch many a time. 
Oh…you can sometimes spot the bad places in the wood by holding it up to a flashlight…then you can place your cuts around the bad spots.