Ultrasound velocity measurements of the orbitally-frustrated GeCo$_2$O$_4$ reveal unusual elastic instabilities due to the phonon-spin coupling within the antiferromagnetic phase. Shear moduli exhibit anomalies arising from the coupling to short-range ferromagnetic excitations. Diplike anomalies in the magnetic-field dependence of elastic moduli reveal magnetic-field-induced orbital order-order transitions. These results strongly suggest the presence of geometrical orbital frustration which causes novel orbital phenomena within the antiferromagnetic phase.