Nice artwork! Are you able to share what the project is about? (I personally like anime styled artwork myself.
Yes, the clipping mask is probably the problem. Clipping takes *all* of the following layers (not just the next single layer). That is why I always put the pupil second last and the eyeball (mask) last and nothing following. I use the eyeball to mask the pupil. (I usually also put eyelids on top, which may seem unnecessary, but I find the combination of the two is safer - the eyelids/eyelashes you want in front of the pupil, but sometimes the pupil can sneak out lower or above the eyelids/lashes, so the eyeball as a mask guarantees that does not happen.
So to fix it, just move that extra layer up higher under the same parent.