。
She made an excuse for being late.
Literal
She [topic-は] late came excuse [object-を] did.
遅れてきた言い訳をした — 遅れてきた is a relative clause ('having come late') modifying 言い訳, tying the excuse directly to the action of arriving late. Compare with the simpler noun-based pattern 遅刻の言い訳 — both mean 'excuse for being late,' but the relative clause version is more descriptive and specific.