I am having same problem. Except, my Media Cache folder has the cache files (.cfa) of videos that exist on my C: drive but have never been imported into Lightroom CC. Some of these movies are video files that I have put on a micro SD card that I've loaded into my machine (a Surface Pro 3 w/ small 128GB hard drive).
A few weeks ago I deleted the cache files, and freed up ~35GB of drive space, but when I began working in LR CC again this weekend, it apparently re-cached the files.
Again - these were movies that I *never* imported into LR. They just happen to exist on my computer. I am pretty proficient with LR, having used it since LR3, but there could be something set up in my preferences that makes LR CC want to go look for thee files.
That is so interesting and odd. In my case I wondered if Adobe Premiere Pro's cache might be affecting it, but that's stored in a different place. FYI, after I deleted the original Lightroom cache files and set the photo cache to 10GB and the video cache to 15GB I re-imported the videos without further mishap (not sure why it was different the 2nd time around). I now have 150GB+ or videos on the paired 7200 Raid 0 discs that are showing up in my Lightroom library and are "scrubbable," keywordable, etc. For now I guess I'm going to keep the videos in Lightroom unless I continue to run into further issues. I AM keeping them in a separate set of video folders so that if I need to move or export them I can do it easily (rather than keeping them together with my photos, which are in folders by date.