I have replaced a couple window regulators on a 06 Jeep Liberty, usually when I have done this its because the window has fallen down.

This time its different. Window goes up and down but stutters. Took door panel off and hit window button and the screwed wire came up between the door frame and window.

Is this something that means the whole regulator/motor assembly needs to be replaced again, or did some attaching hardware come undone?

Its the front passenger window.

After doing 3 of these cursed setups I vowed never again- what a crap design. If the wire guide popped out of the motor casing, I would buy another assembly. Many attempts to put back together resulted in wasted time. The first time I did one, Mopar actually had an entire kit which included the glass along with everything else inside the door to control the windows movement, as well as the switches. I cleaned and moly'ed the side tracks of the door as well. I wish you the best

Sounds like a couple different "common" problems with those 1st gen Liberty's.
Drive cable overextending is because end of cable has separated from lift plate, usually window will no longer be attached to regulator.
Mopar made a repair kit for this where you replace just lift plate with new cable assembly, reuse rest of regulator and motor.

The chatter is usually due to front channel pinching glass too tight.
Once window removed you can spread out the channel to lessen tension on glass then reinstall glass run weatherstrip, lube front glass run w/strip can temporarily repair condition.

Thanks for the info guys. I might just buy a new one and replace, then assess and repair the old one and keep as spare.