I've been having this issue for a while now across multiple Mac devices whereby when I export Canon C100 footage that I have edited in Premiere CS6, red (or sometimes green) flashes appear intermittently throughout the exported video. My current Mac specs are:
I've read pages and pages of posts on various forums about people having the same problem as me and on each occasion there seems to be no concrete answer on what the problem is. The only constant seems to be that the problem is made worse when adding effects to the footage. Not in my case, I get these red flashes regardless of whether I add and effects to the footage or not.
Now, the Canon C100 creates separate files when you record footage over 2GB in length. These files are then automatically stitched together in Premiere when you start the editing process. The red flashing is made worse when using these stitched together files. It seems unlikely that the problem is directly as a result of this as other people using different cameras seem to be having similar problems, however I though it might be worth mentioning anyway.