If the group is mentioned but the statement before إِلَّا is non-affirmative (negative or interrogative), two forms are allowed.
مَا حَضَرَ التَّلَامِيْذُ إِلَّا مُحَمَّدًا
مُحَمَّدًا may be mansub as mustathna.
مَا حَضَرَ التَّلَامِيْذُ إِلَّا مُحَمَّدٌ
مُحَمَّدٌ may instead follow the case of التَّلَامِيْذُ, which is marfu'.
The same two-case rule applies when the complete clause is interrogative:
هَلْ جَاءَ الْقَوْمُ إِلَّا زَيْدًا / زَيْدٌ؟
Both forms are allowed.
The difference is grammatical form; both negative examples communicate that only Muhammad attended.