Over the course of the last few days, I've found a few false positives using Pokecheck.
1) Keldeo, Meloetta, and Genesect aren't immediately deemed hacked. This Genesect for example passes the legality test despite obviously being illegal. http://www.pokecheck.org/?p=detail&uid=408680
2) Zorua and Zoroark sometimes come up as hacked if shiny, even if they're not from the ingame event. This Zorua and Zoroark, both the same Pokemon, are coming up as illegal even though they were bred. http://www.pokecheck.org/?p=detail&uid=419076
3) Evolved Pokemon from Gen 4 onwards are not immediately disqualified as hacked. This Haxorus which the creator has admitted to have created is coming up a legal even though it's in an egg. http://www.pokecheck.org/?p=detail&uid=431177
On a final minor note, have you ever considered changing the "Invalid egg recieve date" to a more specific "Recieve date is in the future" message? I've noticed that the current message is sort of vague and confusing to new users.