Hello everyone, thanks for the answers.
Yes I am indeed scanning negatives with the Nikon Coolscan 5000. It pulls in strip of negatives automatically with a little motor, so you can't manually position the negative inside the scanner or shift the masking.
I discovered the issue when cropping images with Lightroom setting the aspect ratio to 3:2, the cropped area on the right side of the image is quite large:
So I suspect that either the negative is wider than 36 mm or the scanner is cropping something on the top + bottom. Maybe the scanner really crops, since I am not able to scan the perforation or emulsion label on the negative ...?
Have a good day everyone