I am able to replicate your result; 'Auto Enhance' is definitely applied differently to an individual picture than to multiple pictures.
If I select several pictures and choose 'Photos > Add Adjustment Presets > Quick Fixes > Auto Enhance', many of the pictures have clearly-inappropriate Levels settings applied. If I go to one of those pictures and choose 'Reset All Adjustments' in the Adjustments tab, then re-apply the Auto-Enhance (either from the Adjustments tab or from the menu) to just that picture, the Level settings are appropriate to the picture.
Interestingly: if I go to a picture that looks wrong, choose 'Reset All Adjustments' in the Adjustments tab, then undo that reset (via command-Z), different levels settings are applied than the ones I had initially!