I have an issue that I really cannot wrap my head around and was hoping that someone could help me with.
I manage a e-commerce website that is active on multiple markets. Two with a marketspecific domain (mysite.co.uk and mysite.nl) and four with subfolder URLs (mysite.com/ie, mysite.com/fr etc)
The websites have the same content, product pages, architecture etc and managed by home made CMS.
Problem is that when looking in the "GA Search Console > Links to your site" report the mysite.co.uk has about 10K links from mysite.com and the mysite.com/market have about 300K from mysite.com.
The only place where we link from one market to another is in the footer, and I have no idea why the difference is so big. if the mysite.com links 300K times that should be the same towards .co.uk as for the .com/fr.
On the .com sites we have gotten a manual action against Unnatural links to your site, and we can see loss in organic traffic. The only difference between .co.uk and .com in inbound links is the huge amount from our own domain on .com.
Anyone have any idea what have happend and possible solutions?