If the interior is still bare wood and has shrunk causing the sides to curve inward, don't try to spread it with spacers, you may split the strips.
The interior has dried and shrunk relative to the exterior which you froze, at a different moisture content, with epoxy.
Wet the bare interior wood repeatedly with a soaking sponge until the sides expand wider than normal. Let it dry and glass the interior when the kayak is at the right width.
On your exterior bubble. Add a patch of glass feathering the edge of the old glass around the perimeter of the spot, BUT don't sand into the underlaying epoxy coating and into the wood. If you do you will have a dark halo where you've cut into a deeper layer of wood when you add new epoxy.