View time is probably highly heavily skewed towards plays that last less than 3 seconds. (also because facebook autoplays videos without any pause time)
If 60% of viewers play the video for 0-3 seconds, and only 40% view the rest of the video, you're grossly overstation the average view time.
Removing users with less than 3 seconds seems 100% intentional (to avoid exposing the fact that most viewers are not really viewers, they immediately dismiss the video), not an error.