Your webalizer.conf file has the following lines, presumably to hide visits to the S3 stats pages from Webalizer:

IgnoreURL /stats
IgnoreURL /log

It doesn't seem to have equivalent lines for Cloudfront stats, presumably like the following:

IgnoreURL /cflog
IgnoreURL /cfstats

I noticed a couple of URLs in my Webalizer stats that made me check the file.
Anyway, just letting you know. It's not that important as these hits will nearly always be way off the bottom of the top URLs list.

Thanks!