Webmaster Tools internal link counts are wrong

[enotalone]

Looking into the internal links report i see that for our forum's main page it shows 1,086,567 links and for sites main/front page just 552,838. This can't be correct, all pages link to the front page but not ever page in the website links to the forum main page.

I am just afraid that this gives wrong emphasis to the site structure and is one of the reasons we saw a decline in google referrals to every section other than the forum.

Thanks for reading, any feedback and help will be highly appreciated. I tried to bring this up in google forums for webmaster tools but was not able to find any feedback there at all.

[tedster]

WMT has been known to have bad data from time to time (that's putting it mildly) but this is a first for me and it makes me wonder if you do have a technical problem somewhere - such as a canonical issue or two giving some pages more than one URL. I'm admittedly grasping at straws here because I can't come up with a consistent scenario that would create the effect you describe.

If your traffic decline seems to coincide with the report of strange internal link numbers, I would start poking around in the reported URLs area. If there's a problem, it should show itself sooner than later.

[g1smd]

I despair at the crazy numbers that often supposedly pass as internal links counts. Internal redirects also get counted these days.

[enotalone]

Thanks tedster, g1smd. I did not have a canonical tag and the forum main page is indexed both as domain.com/forum/ and domain.com/forum/index.php. I applied the canonical tag and 301 redirect to the index.php version. I went through the website many times in hope of finding a technical error that would cause this miscalculation but so far found nothing.