This is the same problem I am having. I recently changed my skin to an Alex skin, and in game it looks fine. But when I open it in Mine-imator with the Alex model, it will do the same thing shown with Luigi's example. Everything else is fine, but the left arm second layer is weird. But, I do know why it's happening, and it's a simple fix for David to make.
(Also why is it so hard to include photos in posts! Is it because I made this account just yesterday or am I not looking at the right place? Whatever.)
Here is my Alex skin:
Now here is how the left arm texture should be mapped (the yellow boxes are the faces of the arm):
But, it appears the texture map is slightly off, and is mapped like this:
It seems a simple error, that I'm sure David can fix easily as soon as he's aware it's a bug. Until then, I'd suggest that anyone with an Alex skin edit their skin, moving the Left arm section as shown two pixels to the left. Hope this helps Alex users and David if he sees this, and also in proving Luigi isn't being stupid.