Warning. Letting time run out instead of resigning will result in a temporary ban.

This alert appeared on the screen after the game (lichess.org/wKofR2DZ/black#60) even though my opponent did not let the timer run out. We were both running out of time, and my opponent was just trying to keep from making a blunder. Besides, he was obviously leading.

If resources allow, I would recommend fine-tuning the algorithm that determines when time is running out.

There will always be a few false positives. I've received the warning myself occasionally even though I would of course never stall the clock intentionally. As long as you don't see the warning consistently, you have nothing to worry about. In my experience, the system works very well, although it can potentially temporarily ban people with a bad connection even if they weren't stalling the clock.