Its seems faac doesn't handle Adobe XMP chunks in wav files. I don't know much about these, but it appears to be a fairly common chunk of metadata that can appear in all sorts of files. Its tends to manifest itself as a block of XML data near the end of the wav file, preceded by a "_PMT" chunk header. faac mistakenly reads it as part of the waveform, thus given an audible chunk of static in the resultant aac file - usually a fraction of second, followed by some silence - but enough to be audible and annoying.
Interestingly, not all players play this audio glitch, VLC cuts the file too soon. But Quicktime does play it.
I'm looking into a quick fix in code myself, but if you can sort anything, that would be great too. I'll try and add an example file asap.