The pestle is the hand held bit, the mortar is the bowl. Whoever actually transcribed it should have known better. It would have made better sense to write, 'Using a pestle and mortar, lightly crush....' blah blah.
Chemistry lessons at school taught me mortar and pestle. Loads of people say pestle and mortar (*the wrong way round!*) so I suppose that's how the confusion arises. I live in the North East (but don't originate from here) where people eat jam and bread. It surely has to be bread and jam? You can't have the jam before the bread or you'd get very sticky! Same principle with mortar and pestle.
I considered Pedants' Corner for this but decided I'm definitely not being pedantic when I ask: What's wrong with this sentence, written by a chef, in a cookery book?
Lightly crush the peppercorns in a pestle with a mortar.