Most peculiar! I've not seen this particular problem in my playthrough, and have both used silence myself and seen it used by AI (as I've coincidentally just mentioned at
https://forums.larian.com/ubbthreads.php?ubb=showflat&Number=839796#Post839796).
Hopefully some other forum members will have seen it so we can work out if there's a pattern to when this problem happens.
EDIT: Now that I think back, I realise that I've only cast silence myself this playthrough from scrolls, to break into the shattered sanctum without waking drunken bugbears, and again to stop Gut calling for help. The only other instance of silence I specifically recall is the one I mentioned in the linked thread. That last one caused me a problem, but characters could still speak as soon as they popped out of the silence bubble.