I am having the same issue playing as the Klingons

try using espionage and getting the intel level up. not sure why but that sometimes fixs this issue.

Nizzy have you taken the Domination trait for your empire? If you have not you will not be able to subjugate empires, and some empires, I think, like the federation, have extreme requirements to subjugate anyone ever depending on the version of the Federation you are playing. However any Xenophobe, Militarist, even Xenophile empire can subjugate anyone, so long as they have the Domination trait.