macOS Sierra scrolling behavior in Terminal is really weird
This has been bothering me all during the Sierra betas and I couldn't get anyone to address it.

The issue is that there's a minimum scrolling speed now. You can really see it if you use inertia scrolling. You let go and it slows down but then when it gets to a certain speed, it never goes slower than that. And then it stops abruptly at the same time it would have if it had been slowing down normally.

What you're seeing is a side-effect of this. And I haven't found a solution yet. 

And this scrolling behavior is ONLY in Terminal as far as I can tell.

Go to bugreport.apple.com. I am filing more reports.