When a Site Content Type is added to a library and that content type contains hidden metadata columns, those columns are not included in the Content Type within the library.
How to avoid this problem
Do not hide site columns at Site Content Type level, instead hide the column(s) after the Site Content Type has been added to the library.
For more information on hidden columns in a Site Content Type not transferring to the library after adding the Site Content Type click here. Scroll to comment contributor Jing Wang | Microsoft Online Community Support