Ambiguity in natural language is a significant obstacle for achieving accurate text to structured data mapping through large language models (LLMs), which affects the performance of tasks such as mapping text to agentic tool calling and text-to-SQL queries. Existing methods to ambiguity handling either rely on the ReACT framework to obtain correct mappings through trial and error, or on supervised fine-tuning to bias models toward specific tasks. In this paper, we adopt a different approach that characterizes representation differences of ambiguous text in the latent space and leverages these differences to identify ambiguity before mapping them to structured data. To detect sentence-level ambiguity, we focus on the relationship between ambiguous questions and their interpretations. Unlike distances calculated by dense embeddings, we introduce a new distance measure based on a path kernel over concepts. With this measurement, we identify patterns to distinguish ambiguous from unambiguous questions. Furthermore, we propose a method for improving LLM performance on ambiguous agentic tool calling through missing concept prediction. Both achieve state-of-the-art results.