1. If the first list of the Seven Wonders was compiled by Herodotus (Seven Wonders of the Ancient World), then the Parthenon was under construction at the time he compiled it; and even if it had been built, it would have been too new to include. But that argument doesn’t work, because the Mausoleum was done after Herodotus.
2. The criteria for the Seven Wonders appear to have been Big Is Beautful, rather than rewarding perfect structures per se. And perfect temples were probably a dime a dozen back in the day. Per the wikipedia link above, the original term was θεάματα, “spectacles, sights”, and the emphasis was on the spectacular. Antipater of Sidon’s list, which is quoted there, is also all about the spectacular:
I have gazed on the walls of impregnable Babylon along which chariots may race, and on the Zeus by the banks of the Alpheus, I have seen the hanging gardens, and the Colossus of the Helios, the great man-made mountains of the lofty pyramids, and the gigantic tomb of Mausolus; but when I saw the sacred house of Artemis that towers to the clouds, the others were placed in the shade, for the sun himself has never looked upon its equal outside Olympus.
The Parthenon may be perfect, but it is not impregnable, gigantic, a man-made mountain, or towering to the clouds.
3. It has been argued by Anthony Kaldellis (Department of Classics) that the Parthenon was not considered that big a deal in antiquity, and that its reputation as an amazing structure only emerged in Byzantine times, when it was a church. (Bryn Mawr Classical Review 2009.12.18 , https://www.lsa.umich.edu/UMICH/… )