Anchor point centered, but align tool not working

Having an issue where after alining the anchor point to center on a line path, there is still a mystery point at the center of the canvas resulting in an issue where the align tool isn't working correctly. It is trying to use the myster point rather than anchor point. You can see the anchor point is centered on both objects, but the align tool is aligning them incorrectly.
How do I fix this? It hasn't normally been a problem but now I can't seem to get it to work today.
Edit: Detail breakdown



