I figured out this issue on my phone and it may be the same for y'all. I keep seeing this problem on forums (searched for weeks on a way to fix it to no avail) but nobody has suggested the actual audio jack being the issue instead of the Assistant or the operating system. For me it was the audio jack, so test it yourself.
Assistant was only popping up when I listened to music with headphones plugged into the jack, and then I realized it only popped up when I was walking around or on the subway (I live in NYC, so most of the time if I'm listening to music through headphones, I'm also moving). I tried listening to music at my desk at work and -- surprise! -- assistant wasn't popping up. It only popped up when I was moving because the plug was shifting around in the jack or rotating.
I tried to figure out why that may be and I realized none of my headphones have a third sensor on the plug. I don't use mic'd headphones, which come with three sensors -- all of mine only have two. The phone is built for 2 or 3 (the third conducts the mic) and if something inside the receptacle (dust or dirt or lint) keeps coming in contact with the third/mic sensor, Assistant pops up to tell you to configure your mic, and then the headphone plug rotates and the lint stops touching, and then it shifts again and the lint touches it and the Assistant comes back on, wash rinse repeat.
Basically, for me, I just blew into the headphones receptacle with some compressed air and whatever was in there coming in contact with the 3rd sensor is gone now and I don't have anymore Assistant problems. It might work for y'all too.