Purpose: Detailed surgical recognition is critical for advancing AI-assisted surgery, yet progress is hampered by high annotation costs, data scarcity, and a lack of interpretable models. While scene graphs offer a structured abstraction of surgical events, their full potential remains untapped. In this work, we introduce ProtoFlow, a novel framework that learns dynamic scene graph prototypes to model complex surgical workflows in an interpretable and robust manner. Methods: ProtoFlow leverages a graph neural network (GNN) encoder-decoder architecture that combines self-supervised pretraining for rich representation learning with a prototype-based fine-tuning stage. This process discovers and refines core prototypes that encapsulate recurring, clinically meaningful patterns of surgical interaction, forming an explainable foundation for workflow analysis. Results: We evaluate our approach on the fine-grained CAT-SG dataset. ProtoFlow not only outperforms standard GNN baselines in overall accuracy but also demonstrates exceptional robustness in limited-data, few-shot scenarios, maintaining strong performance when trained on as few as one surgical video. Our qualitative analyses further show that the learned prototypes successfully identify distinct surgical sub-techniques and provide clear, interpretable insights into workflow deviations and rare complications. Conclusion: By uniting robust representation learning with inherent explainability, ProtoFlow represents a significant step toward developing more transparent, reliable, and data-efficient AI systems, accelerating their potential for clinical adoption in surgical training, real-time decision support, and workflow optimization.