I've seen real mysteries crafted many times in my 40 years of playing D&D. They pretty much all hinge on the culprit possessing a magic item that renders them immune (and returns false results) to Detect Lies and similar magic.
In a world where a Detect Lies spell exists people who wanted to conceal the truth with have invented a way to counter it, rendering it pointless.
What's weird about that is that you don't need a magic item to foil spells like discern lies and zone of truth, because they only detect whether the person believes they are telling the truth, not whether the statements are actually true. You just compartmentalize information and use deception with the muscle you hire. Eventually if you're able to force the guy at the top to answer questions the spell will out the truth, but that's at the point where you've figured out the clues, completed tracking them down, and are just looking for a definite answer at the end of the investigation. Just some minor obfuscation of the sort criminals use in the real world makes it impossible to just detect lie your way to the end of the mystery.
Look at these exchanges for an idea of what I mean:
"Who hired you?"
"Baron Vanderson!"
dings as truth
Doesn't mean that Vanderson actually hired the guy. Maybe the guy who paid him said he was Vanderson or an agent of Vanderson because he wants to throw suspicion on Vanderson. Or maybe he knows that this thug really wants to get in good with Vanderson's people, so he says this is a favor from Vanderson to get the guy to do it for free. Maybe the hiring person is a commoner who likes making nobles take the blame for nonsense.
"Who hired you?"
"Sir Brandington"
dings as lie
Could mean that the person hiring him was actually working for sir Brandington, but the guy doesn't believe it. Could mean Brandington did hire him, but he thinks someone was playing him. Could mean Brandington hired him, but never identified himself.
"Who hired you?"
"Some androgynous dude in a mask"
dings as truth
Doesn't offer a good lead unless the ability to wear masks and robes is rare in the game world.
"So Lord Salen, are you the head of this conspiracy?"
"Guards, expel these ruffians from my household and inform the city watch that if they come near me again to have them arrested. The only reason I'm not having you arrested now is that you did [previous adventure] before, but I will have no hesitation doing so if you continue with these baseless accusations."
dings as truth
Could mean Salen heads the conspiracy and wants to shut you up, could mean he's innocent and you've insulted his honor.