Competent does not mean infallible, nor does it mean they can't be stupid. Leto is competent. You can argue it all you like but he is an honest, upstanding, hard working young man who is good at his job, smart enough to notice patterns around him, and ready, willing, and able to go off on his own to follow up on his suspicions. None of that has stopped all of his female friends and his girlfriend from fucking around. Why? Because he's yet to have been given a reason to suspect Rose, Cyanna, and Lily are having sex with anyone, and his suspicions of Haylen and Jazon amount to him not finding them. On top of that the game presents him as fairly naive and uncomfortable with public displays of affection and sexual behaviour. So here we are... 15 updates in with a 16th on the way and our competent hero has not walked away or killed everyone because we have a real story.
Your limited imagination does not mean that everyone has to subscribe to your narrow, nonsensical view.