I debugged some more. I think I figured what might be happening. On some of my old NEF files which I had possibly edited in Capture NX2. It might be possible that the crop was from NX2 (and so saved in the NEF), which LR had ignored earlier. When I converted these NEF to DNG, LR still didn't see the crop. However, when I open the DNG in PM, it showed me the crop. I removed the crop (ALT+C) in PM and that made the file reported as corrupted in LR.
Need some experts to confirm if this hypothesis is correct. If so, what do I do to remove the crop? I don't have NX2 anymore.
-Alok