Ride-By Attack and Spirited Charge, by RAW, do nothing. They provide their benefits "when you are mounted and use the charge action". When making a mounted charge, the rider (i.e., the one who is mounted) is not using the charge action. The mount is.
Ride-By Attack is also usually defeated by basic geometry. The Ride-By must continue the line of the charge, which is almost always going to be through your target's square.
If you Trample something with a mount that hasn't got hooves, does it still get a hoof attack?
Pathfinder changed the Mounted Combat feat so that using it is a swift action. Which is used reactively like an immediate action. That would be weird enough, but then they added the Trick Riding feat, which, among other things, lets you use Mounted Combat twice in a turn. I have no idea how that's even intended to work, action-wise. I suspect that whoever wrote Trick Riding forgot or just never noticed that they'd changed Mounted Combat.
(Yeah, I'm playing a mounted archer with a sideline in mounted charger. This is all stuff that I've actually run into.)
My favorite, though, is the lighting rules that depend on the lighting conditions on the observer, not on the thing being observed. Upshot is, if you have one character holding a flaming torch in an large, empty room with no other light sources, another character standing outside the torch's illumination radius cannot see the torch or the character holding it. The character holding the torch can see the character in darkness just fine, though... it's only in the ring of shadowy illumination that you get concealment from the darkness.
For bonus points, combine with the darkness spell that sets the illumination level to "shadowy" rather than lowering it per se. The character in darkness can't see anything, no matter how well-lit, because he's blind, but if he casts darkness on himself, he's no longer in darkness, he's in shadowy illumination, and is no longer blind, and can now see the guy with the torch.
(Pathfinder did fix the darkness bit, but not the fundamental backwardsness of the darkness rules.)