Chiral magnetic interactions in FeSi-type transition metals induce unusual spin structures that offer great potential for computing and storing information1. Emergent helical spin waves and magnetic skyrmions may, for example, be used for data processing and as information carriers in next-generation memories2,3. At present, little is known about the local magnetization dynamics in these materials and the implications for the performance and volatility of future devices. Here we show that collective spin movements spontaneously occur in the helimagnetic ground state of the skyrmion material FeGe. By combining magnetic force microscopy and single-spin magnetometry, we demonstrate that these movements are intrinsic to the system and occur as thermally-activated antiferromagnetic Barkhausen-like jumps. Although such thermal effects are commonly neglected when considering bulk phenomena, they are found to generate significant stochastic perturbations in the nanoscale magnetic structure. The presence of local magnetic perturbations imposes new challenges to the technological usage of helimagnetism and skyrmion materials.