Maybe that's why he brought over Naegi, especially after the last trial.
Bingo. There's no Togami's word against the culprit's, and it makes no sense he and Naegi both would lie when one of them would assuredly die.(Only the culprit graduates.) He's using Naegi as his insurance policy, especially since his credibility is going to be dirt after he admits he tampered with the scene the way he did regardless of his ego.
Also, remember the rule about the furnace room? The clothes of Chi's that have gone missing couldn't have been tossed in the furnace because of the rules set in place to watch it. They're still in the school somewhere, though it's not like Monobear really gave them time to look but it's a good bet they're hidden in the culprit's room. Also, the clothes were taken because I believe they'd reveal Chi was male, and reveal the deception behind the male/female room switch.