According to Cyclops, she's been hanging around the X-Men since before Jean died, so she's kinda been sitting around and watching everyone die for years without helping.
In her defense, I don't think Cipher can phase other people with her like Kitty can. She didn't have any problem giving Dani an invisible sucker-punch when they raided her cabin (she thought Dani was going to shoot Blindfold), but she didn't try to grab Blindfold or anything after Ink knocked her out. Also, despite wanting Graymalkin to hide in the shadows throughout the first arc, she didn't exactly turn him invisible or phase him anywhere with her. Heck, there was a moment when they were about to fight Pierce where Graymalkin expressed his confusion about phasing.
Though that's still no excuse for not phasing through Pierce and causing him to malfunction. We saw that she does the same electric systems breakdown thing that Kitty does when she phases through stuff.
I will admit, however, that if I'm right and she's can't spread her invisibility and phasing to anyone she's touching, then it's a great way to keep her from being overpowered. It's kinda bad enough that she can't be detected by sight, heat, telepathy, or mutant scanners, can pass through all solid objects, and can apparently control who hears her when she talks. If she could make an entire team do the same by holding hands, I'd be done with her.