I was shooting H.264 and on some of my files, certain frames were corrupted (screenshots attached) and sound started hissing, but after 10 seconds the video went back to normal.
I'm on the 5D3123 build from 08-06-2014.
When I switched back to h.264, I turned off:
MLV_rec raw_rec.mo MLV_play MLV_snd
All other modules had been turned off before hand.
I'm using a Lexar 1066x 128GB card.
I was using an atomos ninja 2 as well and those files did not have corrupt frames.
Let me know if there is any other info I can provide.