The spontaneous nucleation and dynamics of topological kink defects have been studied in trapped arrays of 41-43 Yb ions. The number of kinks formed as a function of quench rate across the linear-zigzag transition is measured in the under-damped regime of the inhomogeneous Kibble-Zurek theory. The experimental results agree well with molecular dynamics simulations, which show how losses mask the intrinsic nucleation rate. Simulations indicate that doubling the ion number and optimization of laser cooling can help reduce the effect of losses. A range of kink dynamics is observed including configural change, motion and lifetime, and behavioral sensitivity to ion number.