I've recently moved 2 sections of a site to 2 respective separate subdomains. WMT is now showing the 301s I set up as backlinks into the main domain. The 2 subdomains are also showing themas backlinks.
I checked the 301s using Firebug and they are picked up perfectly as such. WMT even mentions something called an "intermediate link", which I have no idea where it got.
Anyone had any similar experiences of this? Should I be worried?
I'd say there's nothing to worry about here. Reporting a 301 as a link seems to be standard operating procedure in recent times - others have been reporting it as well. Since you've tested the redirects and the http headers from the server are accurate, I'd say have no concern.
I have been purplexed by this for a while. I have a site showing a million links from the non-www to the www, when in fact there's only a redirect from non-www to www - and only a handful links from external sites still pointing at the non-www.