Sometimes CDs would have a long piece of silence at the end of the last song and then another song on the same track.
Other CDs really experimented with the shuffle feature. They Might Be Giants’ Apollo 18 had a bunch of very short tracks that would usually play between songs when shuffle was used.
Broken was first released as a 2-disc set. It was still in a many-fold Digipak case, but also included was a 3" mini-CD that had Suck and Physical (You're So).
The regular-sized CD looked about identical to the 99-track version, but had only 6 tracks.
(It was expensive to do this, and was never intended for long-term production. Later versions were generally as you describe.)
Other CDs really experimented with the shuffle feature. They Might Be Giants’ Apollo 18 had a bunch of very short tracks that would usually play between songs when shuffle was used.