**Please note in "Comments" which knife you are buying the saya for so we can check fit.**
Yes those are intentional. The maker takes a sharp chisel and cuts those into small flaps inside the saya so that the saya "grabs" the knife and holds it in place without the need for a pin. It also keeps the knife from moving around in the saya. It's an ingenious little trick that they came up with and it's a feature not a flaw.
It should fit. If you order them together we'll make sure before we ship. If you have the knife already put a note in the "comments" box when you purchase it and we'll fit the saya to one of ours on the shelf before we ship.