Background: My company manages multiple domains -- our software, our client pages, and our sales site each have a separate domain. Only the sales site is accounted for in Webmaster Tools; and each of these domains are managed separately in GA.
Problem: In Webmaster Tools (for our sales site), the "Links to Your Site" page is made up primarily of links to another domain (our client pages). I'm not sure why this would happen -- and I'm frustrated by what it does to our data.
For clarification: I'm looking at the "all linked pages" page -- so the problem is *not* that I'm looking at our pages linking to us. Rather, Google seems to know that these pages belong to the same owner, and is not making the distinction by domain. (If I hover over the links, in fact, they appear to show the sales domain before the directory & file string -- resulting in a link which is actually invalid, and which has always been invalid.)
It's not the same IP -- and while it's possible that at one point these domains shared an IP address, that would be a minimum of three years ago (more likely 5). The entries in "Links to Your Site" are all from 2011-2013, so that doesn't seem the likely cause. :(