Given that aircraft may find themselves being flown in temperatures ranging from -50°C to +50°C I don't believe that this can be a significant problem or it would have been commented on before.
Slight variations in altitude readings may be due to temperature but all aircraft at a given altitude and temperature would have the same error reading, so the relative heights and separations would remain safe.
Aircraft operating from airfields will generally be supplied with information about local barometric pressure to calibrate the altimeter for landing (QNH/QFE).
It is technically possible that errors can creep in with extreme temperature variations, but at the altitudes where this matters, the pilot should be looking out the window to judge height for landing, not following the altimeter reading into the ground.