Replacing Light Fixture with Extra White Wire
First never attach unidentified conductors until you identify what it is (standard service electrician training). The lone white conductor that was isolated could very well be a switch leg or a non neutral conductor. It should be identified by a phase tape (black, red or blue tape or some other method), but this isn't always done.

So take the lone white wire off of the neutral, cap it off and leave it alone. Then see if they lighting circuit is working properly and make sure no damage was done by connecting it up. If not knowing what that conductor is for is really bothering you, then trace it out or hire a professional to inspect and identify your circuits and make any corrections as needed.

Good luck and stay safe.