Whether a father's name was entered or not depended upon the question asked. If the simple question was "What is your father's name?" the fact that he was dead may not have come up.
According to the extremely useful "England and Wales Marriage Certificate Information" at http://www.dixons.clara.co.uk/Certificates
"If the father of the bride or a groom has died by the time of the marriage then it should say 'deceased' under his name but this is not a very reliable item."