The way I understand Hit's power and Goku's ability to work around it, is that the beginning and (particularly) end of the time freeze aren't instantaneous, but continuous. So it'd go like.
1) Time flows normally
2) Hit stops time. Time screechs to a halt
3) Time Freeze. Hit can move around, attack people, etc
4) Time starts moving again slowly
5) Time resumes normal flow
So Goku applies his extra speed during (4), which Hit isn't used to.
When Hit extends his technique, since he may be applying extra "force" to extend the time freeze, (2) and (4) become shorter and more drastic, and Goku's speed may not be able to keep up. Most people, even Vegeta, aren't fast enough to perceive (2) and (4), but it takes Kaiohken to do it. It is completely possible that even Hit isn't fast enough to perceive (2) and (4).
Jotaro would counterattack during (3), but Goku does it during (4).