I've been having this for a while on my server. I tried this same world in singleplayer and the glitch was gone, but when I took the same world and put it back on the server, the glitch happened again.
How to reproduce
1. Be on a server.
2. Place a bed anywhere above and including 128.
3. Sleep in your bed at night.
4. If you open up the F3 menu, you will notice you are under 0 y, but finishing your sleep or exiting the bed will bring you back normally.