It looks like something is missing underneath the clip. Notice how the clip on the right is obviously higher (top picture), and how the bent clip (bottom picture) is resting on the shoulder of the cylindrical piece that it sits on. So it looks like something is missing underneath it, and when it gets tightened down it's bending the clip over that shoulder as the clip goes past it.

Without seeing a parts blowup I can't picture in my head what would be missing on that part of the head, or how it could be misaligned.

Are those rocker shafts symmetrical, so the flat on the rocker shaft where the clip goes may be in the wrong spot? Or are the clips not symmetrical and it is turned around the wront way? It really doesn't look like the clip is in the right spot on the flat area on the shaft. You might want to take off the rockers and rocker shafts, and check that everything is installed properly. I'd bet that's why everything wasn't tightened all the way.