Portsman only has a bit of a longshot here, but he can declare the second entrant to the room to be heavily involved. Dunno about you, but if Phoenix were defending someone, and eventually found a second person had broken into the murder scene, he'd probably demand that person be brought to the stand somehow.

All that's proven in the virtual horror house can't quite be called definitive if it's only a guess. Possibly more of a contradiction, but they got the building plans directly from the source, so that SHOULD have included the side hallway on its own. (I doubt they'd be hiding secret rooms from the fire department) Since it didn't, it may not even exist. (Hologram badger?)

As Calisto is listening to Edgeworth's story about the knife, all she has to do is deny everything. Instead, she tries to come up with an explanation for how she could know the knife transforms; instead, just say that she never knew. If Edgeworth accuses her of being the Yatagarasu, there's no proof for that either, other than "It's the only way my theory about you knowing the knife trick could work." Also, one of the main points about the knife knowledge being secret is that Detective Badd didn't know about it. However, just speaking in generally, incompetence is not impossible in the AA world.
Officer: Hey, chief! Chief! Take a look at this!
Badd: .....Mhm....
Officer: Look, see! This key...it can transform into a knife!
Badd: Yup, that's great, officer.
Officer: D-...Detective Badd, you're not even looking.
Badd: I'm sure it'll be vital evidence.

Posted this elsewhere, but pull a Damon Gant. "That card you're holding...is illegal evidence!"

As if there weren't already so many similarities between the two. XD If this had happened then it would be official.

I too wonder how a simulated crime scene could prove anything. Even if the building plans are correct, the killer could've said that Little Thief is inaccurate because it is a simulation after all. And there's no way for Kay to prove how accurate the recreation is, without going into the scene itself...

Maybe because unlike Gant, he's not as familiar with evidence law? Or he's just so frazzled at that point any evidence that proves Edgey's point he can't think of anything to counter...