My plane seems to be flying parallel/at an angle to the waypoint in Autopilot

Wouldn’t its course still be on the line, though it’s heading would not align with it?

Looking at the image, it looks like a crosswind from the right, and the plane is oriented slightly in that direction. But it could still do that while on the right course, instead of off to the right. Perhaps the OP has heading mode enabled, and not Nav?