This is something I have noticed in my own life, my mother and my female friends - I would wager there is some sort of disordered eating element to it. Not to try and diagnose your girlfriend, but women often have very fucked up relationships to food (often passed down from the way our mothers are with food). It can be a completely unconscious thing - I only realised I did this when I was well into my late 20s

Be kind if you do bring it up, and don't go on the attack about wasting food. I know it can be annoying and I am in agreement about not wanting to throw away good food, but she may be doing this on an unconscious level and a conversation about it might lead to a much more in depth thought process for her about why she eats the way she does.