Not quite sure. Nutrient imbalance is a very vague, non medical term. Different people imply different notions. Say, fat malabsorption due to pancreatitis (chronic) may cause nutrient imbalance in that fat is being lost from the body. Glutein intolerance may cause iron deficiency anemia, which is nutrient imbalance due to lack of iron. B12 malabsorption will lead to decrease of B12 and nutrient imbalance.
Answered simply. Too much of something and too little of something else - might be the balance of macronutrients like carbohydrates, proteins and fat or abnormal ratios of minerals or too much of one vitamin and too little of another.