What counters Time Alter besides Time Alter and Fatigue?

[KiraWins]

Kiritsugu is in time alter. Obviously Kirei adjusted his time to match him, thus countering it with itself.

Aside from fatigue - what is another counter to this aside from... itself? Is there a way to prevent him from using this?

Any other restriction methods?

[Seika]

Questions, maybe even Badass. Doesn't need a thread to itself.