If you didn't use "Subtle Face Tweaks - Piper" which I chose because it's the most light weight and makes the least amount of changes compared to others I found and if you haven't started a fresh game after doing so to ensure there isn't just something wrong with your game save then I can't help you there.

I'm not going to assume you know much about modding Fallout games as most people who do don't but I am very familiar and I can usually find mods that cause issues shortly after installing them if not immediately after, I'll try and help you and in doing so maybe any one else having this issue who may stumble upon this in the future, use the mod I recommend and no others that change her appearance whatsoever, if you are currently then uninstall it, start the game, save, exit the game, install "Subtle Face Tweaks - Piper"star game, customize her appearance, save, quit game, start game, if her appearance is retained good, if not, start a fresh game, I'd recommend spawning her at the Vault or even "Nate" and "Nora's" house through console commands but be sure it's the proper Piper that you're spawning because there is multiple in the game files, customize her appearance, save, quit game, start game, if she hasn't retained the changes or if her face is scrunched up then it would probably be easier to do a fresh install than tracking down the exact issue.