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Okay TC, the conversation you might of saw was most likely discussing the legality of the moveset. If a Pokemon has a moveset it cannot get without the means of hacking it is deemed "illegal" by competitive battling standards.
They do not check the Pokemon. Some of the 2008 Showdown winners mentioned later that they themselves had used Pokesav to create their teams (Pokesav is actually a Japanese program).
The most "secure" method of checking a Pokemon's legallity is to use it on PBR's wifi. Thats the highest measure of security Nintendo can perform. PBR wifi will not accept a Pokemon if a Pokemon's Secret ID is 00000, has an illegal moveset, more than 31 IVs in a stat , more than 255 EVs in a stat or more than 510 EVs in total. The stupidest things can get by too, such as having a hatched Pokemon be contained in a duskball.
I wouldn't put hatched Pokemon in different balls in an actual tournament though. Too risky. Bottom line, if PBR can't tell the difference, no one can. Just don't use illegal movesets and only have hatched Pokemon in regular Pokeballs.