If this product is not aligned properly, it's a matter of identifying as to why, and honestly it comes down to one of two scenarios:
1. The product was miss-manufactured.
2. Your Mustang has a slight imperfection that is only noticeable during the installation of a decklid panel.
To expand upon the second scenario, we manufacture this decklid panel to fit all Mustangs between 05-09. The idea is every single panel has the same exact dimensions every time its manufactured. Now, if your Mustang came out of the factory with your emblem a quarter or an 8th of an inch off center, or something along those lines, it is virtually unnoticeable until you go to apply what is effectively a very generalized template (this decklid).
However, to begin the process of figuring out whether scenario 1 or scenario 2 is the culprit for the issue, it would require giving out customer service center a call. So unfortunately there is no "fixing" the product. It's identifying which of those two issues is the cause and acting accordingly. Option one is a simple replacement. Unfortunately if it is option 2, there is no simple solution.