This usually happens because kdenlive is not smart enough to deal with multiple types of files, especially different frequency.
If you take a 44.1khz audio track and then add a 48khz track, you will definitely get the pops and clicks.
Use a tool like audacity or similar to do two things, flatten the audio tracks to mono and at least make sure both tracks have the same frequency.
I recommend changing both to 44.1khz.
After I did this and reimported the tracks back to kdenlive, I had no more popping.
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