On Sonar those pops sometimes happen to me when I do punch-in. The "cross-at-zero" setting is on. I expand the wave form on the horizontal to the highest (or close to it) and also expand the vertical. I usually see the punch-in start doesn't start at zero. I pull the punch-in window back until I "see" it cross at zero and stop there. Always no pops after that edit.
Excellent suggestions - thanks a lot. I finally managed to replace that one bum note in what otherwise seemed to have been an inspired take... not sure I could have reproduced the whole thing if I hadn't got the punch-in to work!