This appears to be a mistaken implication retconned later in the anime.

The line in question was spoken in S1EP08 during an anime-only scene expansion about the contents of Sae’s latest publication.

Since everyone knows about the true nature of Sae’s writings, it is implied that she and Hiro are filling the roles of Kensuke and Nanami. This episode aired on March 2nd, 2007.

However, the July 2008 chapter included a strip that contradicted the above, and was later adapted in S3EP01b.

Abbreviated to avoid an extremely tall image.

This sounds like they each had first impressions at the apartments, and therefore first met there, rather than in their childhood. There’s also the additional complication that Hiro’s hometown is in Yamagata while Sae’s is somewhere else in the country.

I believe this was just a case of the anime writers overstepping their boundaries a bit and correcting themselves afterwards. It’s not like they were certain the anime would continue as far as it did and that problems like this would later arise. If you are convinced about the anime canon, though, you could make it work by saying Sae and Hiro met by chance somewhere in Japan as young children but only Sae remembers. However, that season 1 scene is the only evidence you have to assert that they knew each other beforehand.

Edit one year later: Thanks to the graduation OVA, we can call this rumor dead and buried!