When this happens to me, it seems to happen if the turn is too tight (mostly on the SID or STAR/APP), then has to turn in the opposite direction to reach the waypoint. It ends up passing the waypoint by too much distance, and fails to trigger that it has reached/passed it. It has happened on a straight section of the route, but those times were also part of the SID, not the main route.

Note. For now, I just copy the next waypoint on the LEGS page, and paste it to the current waypoint position (LSK1L), then it continues to follow the route.