One possibility is if you mark favorites or rejected ranges on the multicam clip, and make a slight keystroke error you can create 1-frame ranges. You may not notice those until you filter on "show favorites", "hide rejects", etc. Then it looks like a duplicate but it's one frame from the unfiltered multicam.
Another possibility is some kind of timecode glitch. If you enable clip skimming and skim the 1-frame multicam, what does the timecode show? Open the multicam, set a marker at that entry point and skim all lanes of the multicam constituent clips and note the clip timecode values at the marker. Note you can't skim clip timecode on the monitoring angle, so you have to temporarily click the little TV icon on another lane to skim the former monitoring angle.
Do that for both normal multicam and the 1-frame multicam, and see if the exterior multicam clip timecode and entry point clip timecodes are the same. Make sure all Browser filtering is off.
For each one of those multicams, when positioned inside the multicam on the entry point, for each lane do a SHIFT+F to find the corresponding location in the Browser. Check the clip timecode on that point to verify it matches. Is the same frame inside both multicams refering to the same timecode value in the Browser when you do SHIFT+F?
Is all of this MXF or is any of it ProRes recorded on an Atomos? There is a possible issue if doing simultaneous internal/external recording whereby the two files may not be frame synchronized, depending on the below FX6 settings:
Project>HDMI Rec Control must be set to either "SDI/HDMI Remote I/F" or "Parallel Rec." "SDI/HDMI Remote I/F" is used if no SD card media is in the camera (you want to only record on the Ninja V)."Parallel Rec" is used if you are recording internal/external in parallel. That said, "SDI/HDMI Remote IF" will *also* record in parallel, but the internal/external media is not synchronized to frame accuracy. The Parallel Rec option will record internal/external media with frame-accurate sync, but it requires media in both.
There is yet another issue which can cause a 1-2 frame sync discrepancy if both FX6s were jam-synced from certain sources. I don't know what causes that, and since we switch to continuously-connected timecode we haven't seen it. In this case skimming the clips from both cameras in FCP shows the multicam was properly synced on the same timecode value but the two frames are time-skewed about 1-2 frames with respect to each other or the external audio.