It wont fuck the alignment. But it can fuck up your the biting muscles and jaw's joints, nothing disabling or bad, just really painful.
If your jaw is on a normal relaxed position when you sleep, you shouldn't fuck with it.
I had to spend actual money to correct my tense biting muscles and it took years. I actually had to get the 2nd molars removed to get it fixed.
Tho I didn't fuck it up by using a pacifier. I did it by being stressed.
Basically. Don't keep stuff unnecessary stuff in your mouth for long periods of time. Once now and then won't be an issue, but extended periods of time and regularly will be.