When you say “unplugged them” do you mean they were unplugged while you made the audio recording or when you play it back? If your instrumental track is bleeding into the mic while recording the audio, that bleed will be recorded as part of the audio.
I don’t know anything about the AG03, but many audio interfaces can be configured to internally route the output back to the input. Perhaps you’ve accidentally done that?
FYI, highly specific descriptions of what you are doing will result in better responses on the forum than vague & ambiguous descriptions.
If you play back a track and you then see activity on the inputs, there must be a loopback somewhere. It is not cubase itself cause they prevented that so it must be happening outside. Just use trial and error and mute thing to see what causes it. Also have a look in the vst connections what is selected for inputs. Must be pure channel inputs not mix/sub outputs.
I have several interfaces that allow this error (Here Tascam and Motu I have no yamaha)