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A factored Nonlinear Program (Factored-NLP) explicitly models the dependencies between a set of continuous variables and nonlinear constraints, providing an expressive formulation for relevant robotics problems such as manipulation planning or simultaneous localization and mapping. When the problem is over-constrained or infeasible, a fundamental issue is to detect a minimal subset of variables and constraints that are infeasible. Previous approaches require solving several nonlinear programs, incrementally adding and removing constraints, and are thus computationally expensive. In this paper, we propose a graph neural architecture that predicts which variables and constraints are jointly infeasible. The model is trained with a dataset of labeled subgraphs of Factored-NLPs, and importantly, can make useful predictions on larger factored nonlinear programs than the ones seen during training. We evaluate our approach in robotic manipulation planning, where our model is able to generalize to longer manipulation sequences involving more objects and robots, and different geometric environments. The experiments show that the learned model accelerates general algorithms for conflict extraction (by a factor of 50) and heuristic algorithms that exploit expert knowledge (by a factor of 4).