She had a basket full of apples.

Literal

[topic-は] apple [subject-が] full filled basket [object-を] was-holding.

りんごがいっぱい入ったかご ('a basket [in which] apples are filling fully') uses が as the subject of the embedded relative clause. Inside subordinate or relative clauses, が and の can often substitute for each other to mark the same subject — both ringo-ga and ringo-no would be acceptable here — but が is the more direct, neutral choice. The verb 入る takes the past form 入った as a noun-modifier, projecting the resulting state onto the basket.