You have sharp eyes. My build does not have a gap between the cap rail and the gunwale. This is, in part, due to over sanding of the sheer edge after the gunwales were installed, although I still had a small 'ledge' between the sheer and the gunwale. And even though I only applied glue to the top edges of the sheer planks, some glue must have oozed and my clamping caused them to fuse. I started the installation using finger pressure to hold the cap rail in place (as instructed) but fatigued of this and used 2 inch clamps instead. The greater pressure provided by the clamps probably sealed the cap rail to the gunwale as well.
My advice, then, is to glue 2 inch sections (as instructed) using finger pressure and sit still until the glue sets before moving on.
That was a good 'catch' on your part.