Making the skin-on-frame kayak with my friend earlier, we had no issues with our build. The thing you need to keep in mind is that we're both experienced woodworkers. Many of my students in my class or new to woodworking or are coming back to it after a long time.
Sometimes, there are difficulties.
The major one that we've had so far?
What you're looking at is a hole that's been drilled through the sheer stringer on the right and into the frame at an angle. This hole will be fore a screw that will be used to help hold the stringer to the frame while the thickened epoxy adhesive in the joint cures. Drilling at an angle has resulted in a break-out in the frame. This isn't a disaster and can be easily repaired. The bigger issue is drilling edge-on into a piece of 1/2" plywood with a small drill bit and keeping centered in the plywood. Not everyone's eye or hand is quite as steady as it needs to be - practice helps, but we can avoid this issue.
The small jig below is the solution. It's a drilling guide made from some scrap oak. The portion that is in my hand would get clamped to the frame. The other section has a series of holes (Some steel drill bushings from McMaster-Carr or the like would have been a bit better to put where the holes were, but this is adequate.) and goes in front of the stringer. These holes are placed so that they will locate drilled holes centrally in the plywood. Note the notch in the piece that gets clamped to the plywood frame to clear the stringers. Once installed, you drill through the appropriate hole.
Easy and quick to re-position and use.
We're starting to tick along now and frames are going together quickly!