Trust the instructions! The beauty of Oliver + S patterns is that sometimes it seems counterintuitive, but if you do as the instructions say the finish is always beautiful!
So, yes, the facing is stitched with the right side of the facing against the wrong side of the pyjama top. Just as in the illustration (below step 1 Attach The Facing).
Now look at the illustration below, imagine you’ve lifted the facing up and away from the pyjama top. See how the ruffle is neatly sandwiched in between?
So, make sure you are stitching the inside curve of the facing to the pyjama top. This is the side of the facing you basted the ruffle to. (Illustration at the top of that column of instructions).
I always say, don’t overthink it, just trust Liesl to get you there!
Hope that helps.