Canon 5D MkIII Small and Medium RAW files* cannot be used in Capture One Pro. Only full RAW files are compliant at this time.
The software reads these files as compressed RAW formats, so they are not recognized in the workflow. If the small/medium RAW format is the only quality captured, you will need to convert these files to the DNG format (using another software such as Photoshop or Lightroom) in order to work in Capture One Pro.
*Canon’s small RAW image quality provides the flexibility that RAW file processing has always given but in reduced resolution files. Wedding and sports shooters find this feature particularly useful when they are concerned about limited storage space.