If you randomly generate a Vespiquen in pokesav, there will be a 87.5% chance it will be illegal.
Why? Vespiquen evolves from female Combee only. Since there is no way to obtain a legit Vespiquen in the wild, all Vespiquen's must have been female Combee's at one point. Since a pokemon's PID never changes, 87.5% of Combees can never become Vespiquen's.
This means that even though Vespiquen is an all-female species, it must have a gender number that corresponds to a female Combee (roughly 12.5% chance).
Same thing with Gallade's and Froslass'. All Gallade's come from male Ralts or Kirlia, and all Froslass' come from female Snorunt. If you randomly generate a PID for Froslass or Gallade, there's a 50% chance it will be invalid.
As far as I'm aware of, the legit checker DOES NOT detect this.
Pokemon whose entire evolutionary lines are gender-exclusive are not affected. Blissey can have any PID because Happiny and Chansey are also 100% female.