Time Machine not backing up certain changes in file name, format?

I'm running Mountain Lion on a late 2012 MacBook Pro with Retina.

I have an external drive I use for extra storage, as well as one I use for Time Machine backups of both my MacBook HD and the storage drive.

Recently I had to reformat the storage drive and restore from the Time Machine backup. I was surprised to find that some changes I'd made had never been backed up. The two I noticed were:

• In August I converted a couple thousand video files, over a few dozen folders, from AVI to MP4. While the Time Machine backup reflected this for some folders, in other folders I found the original AVI files instead. (My last backup was a few weeks after I converted them.)
• In one folder I'd renamed all of the files (a few dozen video files), a few months ago. In Time Machine, they had the original file names. (These were not videos I ever converted.)

This has got me worried that Time Machine isn't doing the most complete backup. So I have two questions:

1. Is this expected behavior for Time Machine, and
2. If so, how do I go about forcing certain changes (like these) to be backed up?