I have one two disc album that does this. I downloaded it from the CDs, in the proper order. It divides into three, even though in front of each tune the proper order number is displayed, it shows doc one with tune # 1,2,5,6-9,disc two with tune# 3,4 and disc three with the rest. I have never been able to correct this and would love it for someone to provide the correction.
But, my work-around is that I made a playlist with the disc set Title and put each of the tunes on the plaits in the correct order.
I also have a three disc set that "pairs up" two of the discs and shows the third as a single disc. I have put all this up to iTunes oddity or my mismanagement of iTunes.