Looks like a crack in the joint. Looks like it happened in the filler, and didn't pull away the stay. Probably fine as long as you don't see anything to worry about, and aren't mounting brakes on it. If you are then you need to look into it more. It would also be an idea to sight the stay and see if it looks fair (straight where it should be straight, and curved smoothly where it should be).
Alignment can be off in a bike for a variety of reasons like initial build quality, damage, or poorly executed mods. If you can ride with no hands that often isn't a bad sign relative to alignment itself. On the other hand, pay attention to what you think is happening. You should trust the feedback you are getting and what your senses tell you about potential faults. If you ride other similar bikes do they track the same on the same sections of road? Where it is safe to do so, backtrack, riding your same line, and see how that feels.