Hi The cause of the problem is, as you say, Column not found: 1054 Unknown column 'file_id' in 'field list'. Part of the upgrade was to become more consistent with Joomla!. So the database ID name was changed from 'file_id' to just 'id'.
It is most probably caused by an extension that has not been updated.
If you are using AUP, JComments, Komento, Community Builder or Acymailing then extension updates are available.Seehttps://www.jdownloads.net/documentation-for-v3-9/getting-started-v3-9/upgrading-from-jdownloads-3-2-to-3-9#third-party-extensionsfor more info
If you are not using one of those then it is a case of elimination.
Please let us know the situation