The skylight, that were made with aluminum leafing, indicate the time period in which the great hall was constructed. how is this comma used incorrectly in the sentence?

The comma does not belong after skylight or leafing. The clause "that were made with aluminum leafing" is not a clause and includes the verb. It cannot be removed from the sentence, and, therefore, should not be set off by commas. Also, skylight needs to be plural to match case with the verb "were made".  The sentence should read: The skylights that were made with aluminum leafing indicate the time period in which the Great Hall was constructed.

Look at the passages where the author describes the isolation and insanity that dr frankenstein has