Using something like ExifTool or Nikon View NX-I, verify the EXIF data in the NEF file.
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You've probably turned on Auto ISO by accident. On my D810 this is done by pressing the ISO button and then turning the front command wheel instead of the rear command wheel.
This tends to happen more often on photos shot in dim lighting even though there is plenty of light for the camera to capture images at ISO 100.
This shot at 1/500, f2.8 and ISO 100 might have saved the lights from clipping and maybe the subject/ foreground shadows would have been rescuable with an at least 4 stop boost in LR (depends on the camera's DR at ISO 100), but any camera's exposure automation would have judged it to be way underexposed and to hell with the highlights. Does Nikon have a Safety Shift that raises ISO even in M and with the ISO not set to Auto? My Canons will do this in P, but not M.
Thanks for all the responses. I believe I found the issue. The AUTO ISO Sensitivity Control was on, with a max ISO auto control at ISO 1600. This causes the camera to inherently change the ISO if it deems my settings incompatible with the pic, or something to that degree according to Nikon here:
I tested a shot with the auto ISO control OFF and imported it into LR afterward and it kept the setting I had set.