More than 1 million links from one site

[ozsubasi]

Google Webmaster Tools show one site linking to my site with 1,297,033 links. These haven't just appeared, they have been there since just after I started the site a year ago, but I am wondering how it is possible to have so many?
The site that has all these links coming from it is a real estate portal, (estateportal.eu) i.e. it displays adverts uploaded by agents (it's a free service, I have one link back to them from my site in return). I only have 24 adverts and my profile so I don't understand how this could produce so many links, and ideas please?

[ozsubasi]

What I didn't check before posting (but have now) was how many pages this site has indexed, and it has 1,990,000. Looking through the site, at different countries and different areas within those countries, I found that some sites (including mine) were linked on every page I looked at. It can't be beneficial to have so many links from one site pointing to the same page with the same anchor text, so I deleted my url from my profile and my backlink to the site, then checked again and it seems my links are gone. I will have to wait for a GWT update to see if Google has discovered the fact.
I don't know why I didn't look at this before, probably simply because I got used to seeing it there and it didn't seem to be doing any harm. However, I am now wondering if this could be a (or even the) reason for my problems after penguin.

[samsi]

There must be a bug in crawling and reporting. It will be probably fixed in the future.

[bhartzer]

Have you seen the links? Are those links in the footer or really a site-wide link to your site?

I typically only want one link per domain...at least that's what I'm hoping for. So, I would contact that site owner and ask that the site-wide links be taken down.

[ozsubasi]

Have you seen the links? Are those links in the footer or really a site-wide link to your site?
I typically only want one link per domain...at least that's what I'm hoping for. So, I would contact that site owner and ask that the site-wide links be taken down.

Yes I have seen the links, they were visible on every page I checked. I did contact the site owner but received no reply. However, as I explained I think I have removed them now.

[LD]

It seems the issue has been solved. Thread closed, unless the OP requests otherwise.