Thanks for the report! That error message should be improved.
In the meantime: The same query using table aliases works well (though I had to change the JOIN to JOIN EACH to deal with the size of both tables).
Instead of:
SELECT publicdata:samples.natality.mother_age, publicdata:samples.gsod.station_number
FROM [publicdata:samples.natality]
INNER JOIN [publicdata:samples.gsod]
ON publicdata:samples.gsod.year = publicdata:samples.natality.year
LIMIT 100
Do:
SELECT a.mother_age, b.station_number
FROM [publicdata:samples.natality] a
INNER JOIN EACH [publicdata:samples.gsod] b
ON a.year = b.year
LIMIT 100