I'm experiencing this mostly with Voice Isolation as well, but I've also had it happen on clips that weren't using Voice Isolation at all.
Recently, I was editing a video where I needed to use music from another video clip. When I extracted the audio in Final Cut Pro, I noticed the same clicking and popping issues. The only workaround I found was to use another program to extract the audio as an MP3, which worked perfectly (for this issue).
What's particularly interesting is that I was previously running Final Cut Pro 12.4 on macOS Tahoe 26 on my 2020 iMac and never experienced these issues. They only started after I upgraded to an M5 Max Mac Studio running macOS Golden Gate 27.2, despite using the same version of Final Cut Pro.
It's incredibly disheartening. I upgraded specifically to handle heavier projects and improve my workflow. Instead, I'm spending days troubleshooting audio issues and trying to find reliable workarounds.
I've attached a screenshot below showing the audio waveforms from an exported file, where you can see sudden drops that correspond to the audible glitches.
Has anyone else experienced these audio glitches in Final Cut Pro 12.4 without using Voice Isolation, particularly on macOS Golden Gate 27.2? If so, have you found a reliable fix?