Indeed.

The sexual organs of birds cannot be seen from the outside. Perhaps the Pokedex's scanner cannot penetrate the skin of the legendary birds to find out what their gender is?

Another weird thing: Kangaskhan. In the anime, the babies are just young Kangaskhan, and you can see some adults with empty pouches. However, in the game, every Kangaskhan has a baby, even newborn ones. And the baby doesn't count as a separate Pokemon. It's as if the baby were a part of the Kangaskhan's body. Either that or the sprites are messed up.