Guidance doesn't currently get you into trouble, though I'd argue it maybe should when it comes to diplomatic checks if you cast it mid conversation. Guidance is a prayer to your god/source of divine power that your next action will be a success and it has a verbal component, which means every time it is used the caster is saying a small prayer out loud while invoking their divine powers.

While not as overt as Friends or Charm I feel like I'd be fairly suspicious if I were talking to someone and one of their friends started praying to God right when they began asking me if I'd do something for them. At least in a world where I know gods are tangible and frequently answer prayers.

At the same time though you could argue Guidance doesn't influence the NPC, it makes the target more persuasive. Though I dunno how much that distinction would matter to me if I were the one being manipulated with it.