Match Loudness or Batch Process resulting in overlapped audio

One thing that generally makes a big difference to operations like this is everything to do with temporary file space. Ideally you want a separate drive dedicated to this (SSDs are best), and you can use it for temp and media cache files. And check it occasionally to make sure that no files have 'accidentally' been left in it when you're done. You need to keep in mind that in order to do this to multiple files, it has to make a loudness measurement on each one, and if they are large files then they'll take up quite a bit of temp space. The other thing that might help is to reduce the number of concurrent file processes figure from the default 3 to 2. The setting for this is in Edit>Preferences>Data. With anything like this, it's worth experimenting a bit, because no two systems are the same.

I have the same issue running batch processes. It's really annoying and makes Audition unusable for me. I usually run 500 to 700 files per batch and have done so weekly for more than ten years. The glitches appear randomly so if I run the same batch a second time the glitches appear in different files. It seems to be around 5-10% of the files that are affected. And the glitches always appear in the last two seconds of the file.

I've encountered a similar issue on my end. Either that or the audio just sounds very glitchy in general for some reason. When trying to reproduce the issue, a different file gets glitched out each time as well. I've only noticed this with newer releases of Audition.