if it's a single click every few notes, what you are hearing is indeed an analog quirk... namely, the phase of the oscillator waveform is not fixed relative to the volume envelope. The oscillator is running freely with no reset and then when you play a note it triggers the volume envelope which opens up the VCA.
The reason you only get a pop on some notes is that on some notes the envelope happens to hit when the VCO is at the peak or trough of its waveform, and other times the envelope starts right when the VCO waveform is crossing zero.
For low bass notes with fast attack, the VCO signal is moving a lot slower than the envelope is, so it makes a big sonic different whether the envelope lines up with the peaks or zeroes of the VCO.
And yes the thing that sounds like a slow filter opening and closing when you have two VCOs playing the same note... that is slow beating or phasing between free-running analog oscillator... it's something that software programmers have to try very hard to emulate correctly.
One option is just to enjoy it because it's the sound of your oscillators being alive...
if you want to minimize or work with this effect, here are some tips:
1) the closer the two oscillators are to being the same level in amplitude (and same wave shape), the stronger the effect will be. So you can try putting one oscillator at half the level of the other, and set them to different wave shapes, and you'll have less pronounced beating and cancellation...
2) go to Master Menu, Precision Mode, press the Osc2 Frequency button and you can use the Value knob to set VCO2 frequency in precise increments, until the phasing between oscillators is as slow as possible.
3) you can use oscillator 2 to reinforce the strength of your bass sound without any beating, by turning on osc2 sync. If osc2 is only slightly higher pitch than osc1, then you won't have the traditional edgy sync sound, you'll just have a stronger fundamental. Again play with relative levels and wave shapes for best results.