We track individual grains during the discharge of a quasi-2D silo and measure their instantaneous acceleration. This reveals collective deceleration waves which propagate upward through the packing, even though the outlet flow rate remains steady and follows the Beverloo law. Their characteristic frequency shows no systematic trend with aperture size and scales as $\sqrt{g/d}$. We model this scaling with a minimal stick-slip model along the dead zones, in which the relevant length scale is the grain diameter $d$. Introducing anisotropic magnetic interactions promote the formation of vertically aligned grain chains, which increase the characteristic length scale along the flow direction while leaving the transverse size nearly unchanged. This anisotropic elongation leads to a systematic decrease in wave frequency. Our results demonstrate that the internal flow is fundamentally intermittent and governed by grain-scale physics, in sharp contrast with the steady, aperture-controlled flow at the outlet.