I've been studying a particular reaction with DFT, where a transition state and the following intermediate are very close to each other. The change in geometry is rather small and therefore the electronic energies differ only by about ~ 1-2 millihartrees. Still, the TS has the higher electronic energy (everything else would be surprising?), but adding thermal corrections to both structures leaves the intermediate about 2 kJ/mol higher in energy.
Does that make sense? Or is there something I did not consider in my calculations?