Recently though, it happened on the progression from 99 to 100 for archery, and dropped the skill to 15. I was unable to train it away, and no amount of console commands would budge the value from 15. I ended up reloading an old save and when I leveled from 99 to 100 again, it worked as normal.
One thing about the reload, I was able to closely recreate the exact leveling scenario, as I was doing the Archery practice thing with Angi, so I was able to closely control when I leveled and not level randomly in combat. Intrigued by this, I reloaded and went through that controlled leveling scenario four additional times, and out of those four additional tries not one of them went red on the jump from 99 to 100.
So what causes skills to drain into the red in the first place? It's an odd, unexplained game mechanic. The fact that the number goes red implies some intentional design and not just a bug, although with unintended results if it happens at the 99 to 100 jump. Search has yielded mostly conjecture around forcing use of trainers occasionally, and "are you diseased?" comments.
I'm on PC - I assume this affects XBox and PS3 as well.
