This is odd. the file looks to have captured fine in the software stack but every now and then during a sequence the file seems to revert to another image and errors with what it sees.
I get similar issues with Capture and Solve and PAA where every other image is often black and has to try again.

I am using a Canon 80D on StellarMate shooting in RAW converting to FITS.

Its really odd and frustrating as it means the auto functionality is not working properly. I am lost.

I have checked LENR is off on the camera. Anything else that might need changing?

Check the format and make sure it's only set to RAW or one specific format, it shouldn't be two format (e.g. RAW + JPG)