Milligan continues to go by "Milligan" even after he get his memories back because when it comes to his former identity, he feels That Man Is Dead.
- Even after Milligan gets his memories back at the end of the first The Mysterious Benedict Society book, he still continues to go by "Milligan" and his real name is never revealed. Perhaps the events that happened to him changed him so much that he doesn't feel comfortable using his original name anymore.
The "McCraig" in the first book is the McCracken of the later books.
- In the later books, the Ten Men are the group that was originally the Recruiters. The only Recruiter mentioned by name in the original book is McCraig, and in the later books, a McCracken is the head of the Ten Men. Maybe McCracken sometimes just uses a less fierce-sounding name?