It sound like a signal routing problem.
First, what’s the input to the vocal track? It should be the mic input from your digital interface, not something like “stereo out” or the instrumental track. Use the audio track inspector to check this. On this page, the input routing is “no bus”. You want it to be something in your Studio > audio connections > inputs. Of course, you’ll want to use the digital audio outputs coming thru the thunderbolt cable.
Possibly there’s a port mapping issue in Cubase. Maybe there’s some duplication. However, the trouble would not probably not lie here if the instrumental is already recorded and you are overdubbing the vocal. Cubase has a reputation of being tricky to set up with interface hardware. This would be Studio > Studio Setup > VST Audio System > something indicating the apollo unit > check the table on the right.
OK, if that’s not the problem, it could be that the audio interface (or its driver) is mixing the signals onto a single channel. Must check the Console Software. There might be something in the UA software manual about this. It seems that most DAWs and audio interfaces have issues regarding the definition of which responsibilities go where. I suspect you are getting the instrumental track from Cubase to be in the monitor mix on the interface, and then it’s somehow routing the headphone audio to the Cubase vocal track input AND your headphones.
Failing that, there can sometimes be weird behavior over monitoring – the little yellow speaker button in the diagram on this page. I often find the workings of that thing to be confusing and seemingly inconsistent. Then I try various combinations of which tracks have that active and which don’t. Given the Apollo’s emphasis on direct monitoring, I can see how things might get mixed up between its software and Cubase.