I think APFTTU wasn't an 'official' replacement scheme because the issue was minor compared to issues where they chose to do an official replacement scheme (e.g., inaccessible episode on Nadia UE or missing subtitles from an entire episode in the case of Kids on the Slope, as examples).
3 seconds of missing dub audio and a mislabelled disc 1 was likely not seen as significant enough to warrant an official replacement scheme (which would cost Anime Limited money sending out free standard editions or sourcing replacement discs for every CE order). Instead, if it's important to the viewer, they can request a replacement 'quietly' and those who don't care won't bother; saving them money in the long run. So I understand why they have done it this way from a business standpoint.
However, it doesn't exactly reflect well on the company in my view. On a collector's edition from a boutique label I would expect audio tracks to be complete and for discs to be labelled correctly; it's a collector's item after all and while only small errors, it doesn't exactly scream premium or quality. If errors are to occur (and they will from time to time), and even if those errors are small, a company that cares (or at least wants to appear they care), would be out relatively quickly with official communication on the matter (see Second Sight and the Blair Witch Project replacement scheme, due to an audio track being presented in dual mono instead of stereo).
Props to AL for eventually doing replacements, but communication was poor and it could have been handled in a better way in my opinion.
