Chiral magnetic interactions induce complex spin textures including helical and conical spin spirals, as well as particle-like objects such as magnetic skyrmions and merons. These spin textures are the basis for innovative device paradigms and give rise to exotic topological phenomena, thus being of interest for both applied and fundamental sciences. Present key questions address the dynamics of the spin system and emergent topological defects. Here we analyse the micromagnetic dynamics in the helimagnetic phase of FeGe. By combining magnetic force microscopy, single-spin magnetometry and Landau–Lifschitz–Gilbert simulations we show that the nanoscale dynamics are governed by the depinning and subsequent motion of magnetic edge dislocations. The motion of these topologically stable objects triggers perturbations that can propagate over mesoscopic length scales. The observation of stochastic instabilities in the micromagnetic structure provides insight to the spatio-temporal dynamics of itinerant helimagnets and topological defects, and discloses open challenges regarding their technological usage.