Dition: IIRC, she enters after you wipe the floor with her new toys (and underlings, of course). If you have saved right before entering the hall with spiders, redoing the fight will likely help you. otherwise restarting from the latest autosave all but guaranteed to help it move along.
Having friendly spider doesn't break anything, as my rigger will attest to.
Say, you didn't use any of the glitches? Like getting RL Matrix attack? I've never seen things like that breaking anything and, logically, they shouldn't, but I'm always weary of that sort of things and expecting anything.
I have several saves from throughout that fight (I'm a perfectionist, so I savescum to get the optimal results), but I was hoping to not to have to replay the entire thing.
I don't know what glitches you're referring to, so I'm guessing the answer is probably no. I blew up one of the spiders instead of hijacking control of. I did have two spirits under my control -- one that Gobbet summoned herself and one that she stole from the enemy enchanter. The first disappeared after one round, the second I lost and then regained control of, and dismissed at the end of the fight. I wondered if those might be the two neutral parties in question.