I saw an issue several years ago where if the "pre-roll" feature of the Atomos Ninja V was enabled and if you were recording 59.94 fps it could cause intermittent duplicated frames. During those tests with an A7SIII, the internal XAVC-S or XAVC-SI clips did not have the duplicate frames, only the ProRes 422 on the external Ninja V had those. I don't remember if it happened at lower frame rates -- maybe it did.
When "pre-roll" on the Ninja V was disabled, it seemed to avoid the problem. I don't remember the Ninja V firmware version, but there have been numerous updates since then, so it might be good to check and update your firmware version. That said, I don't think the Atomos pre-roll feature is available when recording Prores RAW.
In general, when recording "demanding" media at high data rates, you want to start with qualified, freshly-reformatted media, and do not delete clips on the device. Also do not go over about 80% full on the memory card. Offload all media, then reformat the card within the device, not on a computer. Otherwise the card can become unable to keep up with the incoming data from the camera. This may appear as either dropped or duplicate frames.
The Ninja V has a dropped frame indicator in the form of a yellow kangaroo icon (Skippy the kangaroo). If you *ever* see that icon, something is potentially wrong with your config. See attached image.
In Quicktime Player you can click on the timecode number in the playback controls and it will toggle between timecode, elapsed time since start of clip, and frame number. If you select frame number, on the duplicate frames does it show duplicate frame numbers or does the frame number increment and the frame itself is duplicated?
You can advance Quicktime Player frame by frame forward by holding down the K key and tapping the L key, and in reverse by holding down the K key and tapping the J key.
Likewise, with Quicktime Player set to timecode, the last two digits are also frame numbers. In that display mode, what does that show when going back and forth frame-by-frame over the duplicate frames?
I believe the third-party utility EditReady can transcode from ProRes RAW to various other formats. Whether it would be affected by the same damaged file, I don't know.