By default Adobe Camera Raw will read the EXIF data and apply any in camera settings such as EV compensation, but you can alter the settings easily.
Open an image in the Raw Converter and adjust, then you can save these settings as the Default, then any NEF file will be opened with those settings applied. You may have done this with another image and saved settings that are not good for your present images.
You can even set it to recognise different cameras from their Serial Numbers and apply different settings.
Another possible cause is if you have been using Manual Exposure, then there will be a spread of exposures as the light level and the tones of the images changes with even a slightly different viewpoint, which is why I use Aperture Priority then the camera will reset exposure with every frame and the exposures between frames will be far more consistent.
I fully realise that metering from the camera position is not perfect which is why all camera manufacturers have EV compensation easily available.
The Adobe Raw converter by default will show you exactly what is in the Raw file, some software, and Nikon's View NX could be one of them, automatically applies corrections on opening the images and show you what the software expects you want. I much prefer the Adobe way of working.
Chris