Whether Transformers can learn to apply symbolic rules and generalise to out-of-distribution examples is an open research question. In this paper, we devise a data generation method for producing intricate mathematical derivations, and systematically perturb them with respect to syntax, structure, and semantics. Our task-agnostic approach generates equations, annotations, and inter-equation dependencies, employing symbolic algebra for scalable data production and augmentation. We then instantiate a general experimental framework on next-equation prediction, assessing systematic mathematical reasoning and generalisation of Transformer encoders on a total of 200K examples. The experiments reveal that perturbations heavily affect performance and can reduce F1 scores of $97\%$ to below $17\%$, suggesting that inference is dominated by surface-level patterns unrelated to a deeper understanding of mathematical operators. These findings underscore the importance of rigorous, large-scale evaluation frameworks for revealing fundamental limitations of existing models.