Existing prototype learning-based Multiple Instance Learning (MIL) methods mainly focus on learning a single set of prototypes for each class or generating a generic prototype from the overall data distribution. This design forces the model to compress general and heterogeneous features into identical prototype embeddings, prioritizing general features over subtle but discriminative features. Additionally, these methods often guide prototype updates by jointly optimizing attention score distributions and the distances between instances and prototypes, resulting in prototype biases due to over-concentration. To address these issues, we propose a dual prototype learning MIL (DP-MIL) framework that introduces two distinct sets of prototypes: primary prototypes, which capture general WSI features, and boundary prototypes, which capture discriminative features near the decision boundary. The DP-MIL framework employs three prototype-tailored losses: an alienation loss to encourage primary prototypes to be distant from decision boundaries, an affinity loss to anchor boundary prototypes near these boundaries, and a distance loss to enforce separation between the two prototype sets. To mitigate prototype semantic drift during training, we introduce a prototype joint updating and refinement strategy: for each prototype, we use its corresponding global token to filter out the most similar instances to momentum update the corresponding prototype set, while the boundary prototype set is refined with the mean pooled feature of hard samples. Extensive experiments on four datasets demonstrate the effectiveness of our DP-MIL framework and prototype updating strategy.