Converting from QuarkXPress document

Yah, that'll happen. The way Quark handles master pages is different than how InDesign does, so its best shot is its best guess.  I would first try and reapply the master pages individually to each page (drag the appropriate icon from the Master Page section onto the corresponding pages in the list. Also:  a document may open and no longer be facing pages as spreads. Go to Document Setup and recheck that box. The rest of your problems you will have to tweak as you go. Line breaks and hypehenation will guranteed be different, so you will have to relayout portions here and there. Still, this rude conversion gets you waaaay further ahead than starting from scratch.

Bill, there's no mention of Q2ID but the OP mentions an old document. InDesign can natively open Quark 3 and 4 files which means they would be the better part of 20 years old.

In my experience the Markzware plug-in Q2ID can produce results that vary from very good to just good enough to use as a starting point. The determining factor seems to be what features have been incorporated in the Quark document. Some features may or may not align with InDesign's version of them. It also can vary more depending on what versions of the two programs are being used.

Were you expecting this conversion to be perfect? If so, I'm afraid you were mistaken.