The recently discovered topological fluctuation state provides a fascinating new perspective on the ultrafast emergence of topology in condensed matter systems. However, rather little is known about the physics of this state and the origin of the topological fluctuations. Using time-resolved small-angle x-ray scattering, we observe that topological fluctuation states appear after laser excitation even if the final state does not host stable skyrmions. Simulations support these findings and reveal that the fluctuations originate from the competition between spontaneous nucleation and decay of skyrmions, consistent with Arrhenius-like activation over a potential barrier. Stable skyrmions can freeze out of such fluctuations when the effective temperature of the system relaxes faster than the decay time of the skyrmions. Our results reveal a robust scenario for the generation of topological fluctuation states, potentially enabling their study in a wide variety of magnetic systems.