How do I delete a user from the master database when the user has been deleted from the Server Logins using the SSMS Object Explorer
There's two concepts with security at play here, and in general how SQL Server works. There are Logins and Users, which the differences are discussed a little further in this StackOverflow answer. You've deleted the Logins which is server level, but the Users associated to those Logins still exist at the database level, which has its own Security node you can expand and then a Users node below it.
Whenever you map a Login to a database (to grant database permissions) it creates a User in that database.
Example: