I think what you are getting is maybe footage recorded with different scene settings. Did your camera's F wheel slip on one take? If FCP can't find the pulldown it will stop capturing.
You've probably had a time code break. You probably stopped the camera (powered off) or it powered down. In these cases you want to hit the Rec Check button so it will continue the timecode where it left off
Set camera options to regen timecode. If you use a preset timecode it has to be at specific frame numbers.
Try starting a capture after the camera is rolling a couple of seconds.
Ideally by using timecode in/out points.