Hey, thanks for the report!

I was not able to reproduce it on my end, however there might be another explanation to the described behaviour.

Could it be, that your unity structures (or Progenitor capital ship) were disabled, after the first cast of Chastise?
Disabled means, that they were either stunned, crippled, or actually disabled through structure rotation menu.

All of those conditions would reduce your current unity points, which would then be forcefully substracted from your unity abilities (in your case Chastise), and lead to the ability being locked.

By your description, I would suspect planetary building rotation the most. 

As far as not being able to use it - Chastise requires you to have dominant culture on a planet. Could it be that you tried using it on a planet without dominant culture?

Note - you can easily get dominant culture for a brief period by using the proselytize unity ability, so Chastise has a nice synergy with this other Unity ability.