If you're working with multiple file formats for video post-production, you might have experienced what looks like bizarre Adobe After Effects-style imagery, without ever using After Effects. That's called a dirty cut.
With film it was never a problem, but digital has created new challenges for movie makers. The software (iMovie, Adobe Premiere, Final Cut Pro, or Avid Media Composer, for example) doesn't understand how to render footage from multiple codecs with clean cuts. (An example of a dirty cut effect is shown below, lasting for 24 frames.)
If you want to fix this problem, here's a step-by-step approach.
First, collect all of your assets in one location. Copy the files from your camera to the drive you wish to edit on. External drives are great because they're portable and expandable; but are much slower to work with. I recommend keeping an offsite backup copy (iCloud, Amazon Cloud Drive, etc.) should anything happen to the assets in your editing environment. This is especially true if you're going to capture the footage, or if you're going to delete the originals from the memory card you retrieved them from.
Once you've got all of the files into a folder on your file system/operating system of choice, download an open source program called MPEG Streamclip. It's a useful, free utility that can handle video conversion between most any formats.
From your downloads folder, extract the files to C:/Program Files/MPEGStreamClip folder. If you're using WinZip or a similar tool, make sure to check the box "show extracted files when complete."
Once it's finished unzipping, right-click the MPEG_Streamclip.exe application file and pin it to the Start menu, quick launch menu, or desktop.
Run the program. From the program's main menu, select List--Batch List, or press Ctrl-B.