Was this in conjunction with it not noticing that you passed a waypoint due to the GPS coordinates being off from the waypoint coordinates?

Negative. This was on a different occasion when it was correctly tracking my path.

However, there's a chance that I may have had to twiddle the knob during the start of the trip (i.e., I was already underway when I activated GPSapp, and I twiddled the knob to make it reach the current waypoint).

But when I noticed the "counting up" thing happening, it was tracking correctly and following waypoints correctly.