Hi, all – I’m a brand new user to Cubase… switching over from ProTools on the advice of a few colleagues… praying it wasn’t the wrong choice! I’m trying to accomplish something very simple here and cannot for the life of me figure out what it going wrong. I’m attempting to record vocals to an imported instrumental track – so the session is just 2 audio tracks – one for the instrumental and one for the vocal. Recording through an Apollo MkII Twin on MacBook Pro, macOS Catalina 10.15.4.
The issue: whenever I record on the vocal track, the audio from the instrumental is being recorded onto the vocal track. It’s not headphone bleed… it’s actual clean audio, basically a duplication of what the instrumental track is, but on the vocal track. The only way I can get this to stop is to mute the instrumental entirely, which (for obvious reasons) isn’t a practical solution. Someone please help!! 
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.