We present experimental results on the relaxation dynamics of vesicles subjected to a time-dependent elongation flow. We observed and characterized a new instability, which results in the formation of higher-order modes of the vesicle shape (wrinkles), after a switch in the direction of the velocity gradient. This surprising generation of membrane wrinkles can be explained by the appearance of a negative surface tension during the vesicle deflation, which tunes itself to alternating stress. Moreover, the formation of buds in the vesicle membrane was observed in the vicinity of the dynamical transition point.