Large language models (LLMs) represent words through contextual word embeddings encoding different language properties like semantics and syntax. Understanding these properties is crucial, especially for researchers investigating language model capabilities, employing embeddings for tasks related to text similarity, or evaluating the reasons behind token importance as measured through attribution methods. Applications for embedding exploration frequently involve dimensionality reduction techniques, which reduce high-dimensional vectors to two dimensions used as coordinates in a scatterplot. This data transformation step introduces uncertainty that can be propagated to the visual representation and influence users' interpretation of the data. To communicate such uncertainties, we present LayerFlow - a visual analytics workspace that displays embeddings in an interlinked projection design and communicates the transformation, representation, and interpretation uncertainty. In particular, to hint at potential data distortions and uncertainties, the workspace includes several visual components, such as convex hulls showing 2D and HD clusters, data point pairwise distances, cluster summaries, and projection quality metrics. We show the usability of the presented workspace through replication and expert case studies that highlight the need to communicate uncertainty through multiple visual components and different data perspectives.