The invisible ATB gauge on that particular enemy is intended. I might add something to the scan data that says that if I haven't already, and I'll look at the dialogue there as well to see if I can drop a hint there. I'll check the Sphinx's dialogue as well. All the changes should drop with the next patch/version.
I could've sworn I added the "Not independent item" tag. It shouldn't affect the Shuriken's battle functions, but I'll get rid of it with the next patch.
For the Red Cap fight, the Restore Matrix is powered by the Rauthaz, so you've got to take that down first. Is the Rauthaz going down properly?