。
Maybe she still hadn't finished her homework.
Literal
[topic-は] still homework [object-を] had-not-finished [explanatory-のかもしれない].
終えていなかった is the past form of the negative resulting state — 'was not in the state of having finished.' Combined with まだ ('not yet') and the speculative ~のかもしれない ('it might be the case that'), the sentence gives 'maybe she hadn't finished it (yet) at that point' — narrative-style speculation about a past moment. The のかもしれない here softly hedges what might already be the case, reasoning from observed signs.