One important practice is to avoid drag and drop for files. It was recommended to actually clone the card through the disk utility. I don’t know if this is your problem but I know that when you drag and drop some of the folders could be out of order. It’s rare but it could happen. However, I don’t think this would affect the card. Another simple reason for the red x’s would be that your camera is not in the same system format that you shot them in. You need to play back clips in the same format they were shot in.
P.S. Did you try to repair the clips in the camera?