It happens with the "real" Quicktime player too (come on, Apple, fix this already)...
It
IS annoying that MC downloads and names Quicktime files with names longer than 64 characters, when it should
know that it won't be able to play them... One thing that can help is to not use Quicktime or Quicktime Alternative to handle MP4 media. That won't help with podcasts that actually use a MOV container, but since Quicktime is broken and other filters
can decode MP4 you'll have better results if you don't use Quicktime to handle MP4 files.
MC will use Quicktime if you have MP4 unchecked in
DirectShow Playback Options. If that box is checked, MP4s will be handled by the the DirectShow engine instead. Just make sure you have
appropriate filters installed for MP4 decoding, and make sure that box is checked.
As I said, that only helps with MP4 podcasts (and M4A and M4V which are the same thing). For MOV podcasts there isn't really a workaround other than manually renaming the files after they download.