The AP-3 frame will be the third frame you get, as part of the story so it isn't missable.
Some way through the story not too long after you defeat your third boss your main path will be blocked and Joule will mention you need to find another way around. Follow the waypoint to an abandoned Crawler which is where you will get this frame. Go back outside and a waypoint should lead you to some rocks blocking a doorway, use your new frame to break these.