First, make sure you are working with copies of the video files on your hard disk. Movie Maker can have a hard time if video is being pulled from an SD card on the fly.
Additionally, the support of .mts files in Windows Live Movie Maker 2011 is not as good as it is in Movie Maker 2012. It seems that this is manifesting itself as footage that gets marked as incompatible/corrupt occasionally in your case.
If you have the requisite hardware, you might try installing Movie Maker 2012 in place of WLMM 2011. If you don't meet the system requirements (driver level, etc.), then perhaps you could convert the .mts files to .wmv format using something like Freemake Video Converter (freemake.com). That can really help, since Movie Maker works the best with .wmv video.