Some real-world domains, such as Agriculture and Healthcare, comprise early-stage disease indications whose recording constitutes a rare event, and yet, whose precise detection at that stage is critical. In this type of highly imbalanced classification problems, which encompass complex features, deep learning (DL) is much needed because of its strong detection capabilities. At the same time, DL is observed in practice to favor majority over minority classes and consequently suffer from inaccurate detection of the targeted early-stage indications. To simulate such scenarios, we artificially generate skewness (99% vs. 1%) for certain plant types out of the PlantVillage dataset as a basis for classification of scarce visual cues through transfer learning. By randomly and unevenly picking healthy and unhealthy samples from certain plant types to form a training set, we consider a base experiment as fine-tuning ResNet34 and VGG19 architectures and then testing the model performance on a balanced dataset of healthy and unhealthy images. We empirically observe that the initial F1 test score jumps from 0.29 to 0.95 for the minority class upon adding a final Batch Normalization (BN) layer just before the output layer in VGG19. We demonstrate that utilizing an additional BN layer before the output layer in modern CNN architectures has a considerable impact in terms of minimizing the training time and testing error for minority classes in highly imbalanced data sets. Moreover, when the final BN is employed, trying to minimize validation and training losses may not be an optimal way for getting a high F1 test score for minority classes in anomaly detection problems. That is, the network might perform better even if it is not ‘confident’ enough while making a prediction; leading to another discussion about why softmax output is not a good uncertainty measure for DL models.