There is really very little of the hard science that could be called "outdated", even then it is mostly stuff for which evidence was simply not available (the molecular biology in episode 2 for example is very rough and there has been tremendous progress made since 1980, some of it is mentioned in the 10 years later update) or omissions (the formation of the moon is not clearly mentioned in episode 4, hence there is no mention of the Giant Impact Hypothesis, the prevailing theory about the origin of the moon).
Additionally some of the planetary science is not up to date with the groundbreaking discoveries of various spacecraft and landers we send out since then (Galilio, Cassini-Huygens, Pathfinder/Sojourner and the MER missions etc.), again some of it is mentioned after the fact, most prominently the later parts of the Voyager missions (ie the Pale Blue Dot Photograph) as they ventured into the Outer Solar System.
Also we know now that the Milky Way is a barred Spiral Galaxy (evidence for the bar was discovered by the Spitzer Telescope), again mentioned in the 10 years later segment (at least the theory, if not the evidence) with only two major stellar arms (instead of the previously thought of four -> discoveries made through the Spitzer imagery).
Really the biggest thing is Pluto's demotion to dwarf planet and the creation of that category of stellar objects (the Plutoids), as in Cosmos it is referred to as a regular planet.
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