Is there a reason why a post with three links should be blocked when the link 'Number of Allowed Links' is set to four?
I've included a blurred example below to show the type of genuine post gets blocked for link counts violation incorrectly - you can still read the reason and see the number of links in the blocked post.
Is the system reading the HTML and pattern matching links twice because "something.com" is actually "<a href="http://www.something.com/">http://www.something.com/</a>" underneath?
Your assessment, without stepping through the code, seems to be consistent with my test, the anchor text and href seem to be counted independently. I have filed this for review:
'#101481 Link Counts Automation Plugin Over-Counting Links' has been completed for 10.1.