Could it be that some of the pieces were sliced thicker than the others? I've never tried baking pears but I would imagine they'd cook slower than apples too. Maybe if you sliced the pears thinner than the apples ... ? Different kinds of apples are firmer and take longer to cook than others too, and some aren't good for baking at all and will turn to mush.
When I make apple pies from scratch, I try to make all the slices the same thickness, fairly thin. I start it off at 400 degrees for about ten minutes, then turn it down to 325 and let it bake very slowly until it's completely done. If the edges get a little too brown, you can put foil over them