I don't understand what you're saying.

Literal

I [to-は] your say thing [subject-が] not-understand.

君の言うこと ('the things you say') uses こと to nominalize 君の言う ('the [things that] you say'). 分かる ('to understand') takes が for the thing understood — it's an intransitive state verb, not a transitive action. A common way to signal communication breakdown.