Yeah, I almost feel like Vader telling the troopers to “Stop” might help with the audience head scratching. It easier to digest Vader choosing not to pursue rather than not being able to. You could argue Vader wants him to flee with his allies in hopes of it leading to other surviving Jedi, and those that are helping them hide.

On a more personal level, maybe Vader is just a little disappointed by the encounter. I imagine Obi-Wan was not in the condition he was expecting, beating him was much easier than he thought it would be, so a part of him wants to enjoy the hunt a little more.