Final Cut Pro X can use clips with non-square pixel aspect ratios. However if QuickTime movies don’t have the correct flags set internally, there is no way to tell Final Cut that a clip’s pixels are anamorphic.
In Europe since the late 90s the majority of standard definition video has designed to be viewed on widescreen TVs. Instead of coming up with a new TV standard, a signal was added to broadcasts that told TVs to stretch the source 720 pixel-wide image from an old-style 4:3 image to a modern 16:9 widescreen image. This is the ‘anamorphic flag.’
Many QuickTime manipulation applications don’t set the anamorphic flag on clips, which means that Final Cut doesn’t show the clip in 16:9 widescreen – the clip displays as 4:3 so everything looks tall and thin. In Final Cut Pro 7 and earlier there was a quick way to define clips as having anamorphic pixels, that feature isn’t available in Final Cut Pro X yet.
There are two strategies to fix this: use an application to re-encode the clip that sets the anamorphic flag correctly, or use an app that can manipulate settings within clips without any re-encoding.