*UPDATE* Read This if you're interested in the 5D Mark II firmware 2.0.4 apparent issue.
Thanks for the link wickerprints.
Nothing is broken
After reading some comments and talking to folks, it turns out this is normal behavior for a Macro lens.
Explanation From Dave
If these people bothered to dismount their lens, and just look through the barrel when changing focus, they’ll notice that the 100mm Macro does this even when not mounted to any camera. All Macro lenses do this…the Aperture Diaphragm closes down as focus approaches MFD…this is what people refer to when they say that the “effective aperture” is smaller at macro distances
Now there is still some disagreement in the comments section whether or not it's truly normal. I have sent a mail into Chuck Westfall in regards to the issue.
The people critical of me posting this as fact need to see the “?” after the title of the post. I was questioning whether or not there was actually an issue and letting people discuss it. My technical expertise on the subject is lacking and I was seeking an answer.
Stuff like this is worth discussing and having a record of.
In the future, I'll make it more obvious that I am asking, not telling.