I have seen this kind of thing in the past and have been able to solve it by purging the cache. It happens most often with codecs that take a bunch of CPU power to decode like Canon's MXF and other formats. I even saw it a couple of times using CS6 and Arri RAW files.
Let us know if the purging everything clears up the problem.
If it doesn't you could always transcode the footage to a suitable 10 bit or better DI or render to an 16 bit image sequence. That's what I do with a lot of my keying work because I like the additional color depth and control and you can't beat image sequences for reliability.
Rick, many thanks for your clear and helpful answer. I had thought my next step was to export, although I had not thought to use image sequences. I'll also try the purge. Best regards.
Rick: here's an update.
Purging did not solve the all the green artifacts. I found that making identical duplicate Keylight effects on the footage did remove some of them (go figure). In one case, it took 3 copies of the identical copy of Keylight to avoid the green artifacts. I sidestepped the whole infuriating issue by first exporting the MXF files from FCP as ProRes, and then using Keylight in AE. No wonder I drink too much... regards.