We perform for the first time a dynamical system analysis of both the background and perturbation equations, of $\Lambda$CDM cosmology and quintessence scenario with an exponential potential. In the former case the perturbations do not change the stability of the late-time attractor of the background equations, and the system still results in the dark-energy dominated, de Sitter solution, having passed from the correct dark-matter era with $\gamma\approx6/11$. However, in the case of quintessence the incorporation of perturbations changes the stability and properties of the background evolution, and the only conditionally stable points present either an exponentially increasing matter clustering not favored by observations, or Laplacian instabilities, and thus not physically interesting. This result is a severe disadvantage of quintessence cosmology comparing to $\Lambda$CDM paradigm.
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