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We study non-radial oscillations of neutron stars with superfluid baryons, in a general relativistic framework, including finite temperature effects. Using a perturbative approach, we derive the equations describing stellar oscillations, which we solve by numerical integration, employing different models of nucleon superfluidity, and determining frequencies and gravitational damping times of the quasi-normal modes. As expected by previous results, we find two classes of modes, associated to superfluid and non-superfluid degrees of freedom, respectively. We study the temperature dependence of the modes, finding that at specific values of the temperature, the frequencies of the two classes of quasi-normal modes show avoided crossings, and their damping times become comparable. We also show that, when the temperature is not close to the avoided crossings, the frequencies of the modes can be accurately computed by neglecting the coupling between normal and superfluid degrees of freedom. Our results have potential implications on the gravitational wave emission from neutron stars.