I just noticed that one particular site has almost 7000 backlinks linking back to our website. The site is something like a news aggregator and for each post they created around 20 (sometimes much more) backlinks back to our page and they basically linked over 400 pages.
I am beginning to get concerned that this amount of links might harm our page. They seem to have more backlinks to our page than all the other pages combined and more backlinks that our website has pages.
We have seen a massive negative effect going on for quite a while and the PageRank seems to have dropped to None (Not even 0). But I am not sure when and why exactly that happened seeing that PageRank updates take quite a while to appear. The site linking to us is otherwise pretty reputable and doesn't seem to be having any problems with their rank. (PR 6 actually)
I was thinking of using the Google disavow tool for this site, but I don't want to make things even worse. Do you think these are harmful? If so, how do I fix this? Thanks :)
If you think that these external links pointing to your domain are harming your site, I would defiantly submit the domain in question using Google's disavow tool. To have that many links in any case doesn't look natural.
You should Disavow those links but before doing that be cautious about that Tool. Matt Cutts said that using this tool with less caution may harm your site.
After Disavowing those links, just request Google to reconsider your site and you would feel the positive effects within one or two months.
Having up to 100 links from the same domain is ok but having 300 is alarming and will hurt you webpage performance at search engines. I think you need to analyze you backlinks and try to remove them if possible. Disavow tool is the last resort and i would never go for it until i have no other option.
Sounds kind of spammy to me.... How does the page rank in terms of quality and the quality of the backlinks of that page? - Checking the backlinks of the page that links to you is the easiest way to figure out if a backlink from a certain site is worth it - you might want to use a tool like majestics.com for that.