Yes. Buyers can leave you negative feedback for any reason. It depends on a case by case basis if the negative is removable.
For instance, if in your situation the buyer leaves you a negative and says "I never got my item" you have a chance of getting that removed if you call eBay and explain the situation to them with valid proof.
But if in that same situation the buyer leaves you a negative and says "bad customer service", that feedback will stay because it's vague and can be in regards to other things aside from the non delivery.
