False rule: every noun after illā must be accusative.
Correct analyses:
«مَا جَاءَ إِلَّا خَالِدٌ»: Khālidun, nominative subject.
«مَا رَأَيْتُ إِلَّا خَالِدًا»: Khālidan, accusative object.
«مَا مَرَرْتُ إِلَّا بِخَالِدٍ»: Khālidin, genitive after bi-.
All are mufarragh and follow their actual governors.