Hasbro addressed the how's/why's they sometimes don't give the mix everyone thinks is "ideal" in their battlepacks in a recent Q&A... It has to do with what molds are at what factories and things.
I've heard them address this firsthand at Toy Fair and other events where Hasbro exhibits. They've most commonly addressed this when we talk about Basic Figure reissues and you start to understand why one version of a character is chosen over another that collectors might consider to be superior.
But this particular situation seems to me like a case of Hasbro's exclusives group not communicating with their general retail group. There are actually some divisions within Hasbro along these lines. It seems to me as though these groups were not communicating when they were planning out the general release battle packs and the exclusive ones. Especially when you consider all of the Jedi that were in the arena battle that have figures besides Aayla Secura. Look at this:
-Nikto Jedi (either version)
With that many characters at their disposal that are ready for reissue, this just comes across as very lazy on Hasbro's part.