I'm also experiencing these noises and I think we have to just live with it for now. However, in your situation, if you're on Windows, you can easily avoid the issue. I created the free VST plugin AW_multichannel_channel_switcher_2x_mono exactly for this situation.
When you wanna record a source with more than one mic (to be able to pick the best sounding signal during mixing), instead of recording the resp. no. of separate tracks, rather record all source signals into a single track configured as multichannel. In your case, recording two signals at once, you don't have to especially configure anything. However, instead of recording two separate mono tracks, record into one track where you choose stereo as the input (channel 1/2). The first mic's signal will be the left channel of the 2-channel (not really "stereo") recording and the second mic will be the right channel. My plugin allows you to only listen to either of the two in mono, seemlessly muting the other one. The plugin allows you to further tweak the individual levels retroactively to compensate for level differences in the original recording. So, instead of having to mute/unmute the two signals (not providing perfectly seemless a/b-ing), you can a/b absolutely seemlessly by toggling the "active channel" slider. You can even automate all sliders if necessary.
I've created several variants of this plugin to easily a/b various no. of mono or stereo channels, like if you recorded a voice or instrument with up to 4 different mics or if you wanna compare up to 4 stereo signals.
If you wanna a/b more than 2 mono signals you have to set the track to have more than the standard 2 track channels in its track routing window and also set the track's input to the according amount of (multi-)channels.
Regarding your current situation again: Even now that you recorded two mono tracks of your sax you can retroactively combine the two mono tracks into a single stereo file (there are actions to accomplish this) and then use the 2x mono switcher to conveniently toggle between the two signals. One cool thing is that while using the plugin the you may also be recording multiple takes and still easily toggle the different source channels. It gets massively complex if you try to do this whithout the plugin with let's say 4 separate mono tracks.
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Wild noises when unmuting tracks
Linear Mode
