。
He clearly hadn't understood what I said.
Literal
Clearly he [topic-は] I [subject-が] said [nominalizer-こと] [object-を] was-not-understanding.
私が言ったこと — the whole subordinate clause ('the thing I said') nominalized with こと so 理解する can take it as an object. が inside the subordinate clause marks 'I' as the internal subject. 理解していなかった is the past negative of the progressive — 'was not in the state of understanding.' A common way to describe non-comprehension in past time.