Duplicate field within hidden system content type

Hi Yaron_Ben_Shalom, did you already think about to migrate your concerned data to MODERN SharePoint Sites? Two main reasons i can imagine: 1) a "duplicated field" within 2 content types sounds crazy and if ever possible SharePoint likes only unique column names. I guess, there are certain site columns, and you should try to first delete the already empty and error causing site column - if this site column is empty and not linked with any content in several sites. If this site column is deleted, and the next step you can delete the content type. Every linked data in a site column within a content type causes your described error, i guess.

2) In SharePoint online and modern SP Sites i already have all content types and site columns within my SharePoint Admin Center. If you only are a Site Owner and no Site Admin, maybe you don´t have permission to change content types and maybe your SharePoint is now in transition from classic 2013 sites to modern Sites? I can only guess. The link error can be in the hidden part of your root site, maybe in a lookup (site) column and there is the relationship option within this special column. Did you already deactivate this relationship option (check box) within the site column settings? If you are able to look into the site column settings, you can deactivate this field link and then you can possibly delete that double trouble column... But before deleting make sure that there isn´t any related data in this list!! No disclaimer on my side. 

Hope that helps a bit, greets, Eva.