Magento site had weird characters in the top of Magento Connect

These files are mostly likely meta-data files for OS X's HFS+ file system. See this entire thread on the Apple Stack Exchange for some good starting points if you're interested in the details.
Oversimplifying things, when you create a tar archive on OS X these files are included along with the "real" file. This allows Macintosh specific meta data to survive the trip into a file format that wasn't created specifically for the Mac. If you untar the files on a Mac, the meta-data is preserved. If you untar the files on a non-Mac, the ._ files are generated in case the meta data is needed.
My guess is, at some point someone tared up those files to move them to the production server from their Mac, which brought along the the ._ files for the ride. You can avoid this in the future by running
export COPYFILE_DISABLE=true
from the terminal prior to copying the files. Details on this here.
(It's pretty bizarre that PHP would attempt to include those files instead of the correct files — did you debug this far enough to know why/what connect through it was doing?)