tedster - 3:05 pm on Jan 17, 2012 (gmt 0)
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.