Here's a different answer.
First: Play DMG 1E Appendix A. Use it to design a dungeon adventure. The idea here is that in design mode, you're still "walking through" the dungeon the way, or at least one potential way, the players might walk through the dungeon. The problem with starting with an idea then building logically around it is, you're starting already knowing the answer. Make use of Appendix I (dungeon dressing), give roughly a 1 in 3, 1 in 4, or 1 in 5 chance of there being one or more items from Appendix I whenever you hit a side passage or empty room. Add a direction component where appropriate. (d8: n, ne, e, se, s, sw, w, nw). The idea here is to experience how a simple sight, sound, or smell will nudge you into a particular course of action.
Second: Adapt it to your genre. Swap out the wandering monster list with your cast of NPCs. Keep in mind, many monsters have built-in motives, albeit typically base and uninteresting ones. When you make it human NPCs, you have to be more conscious about giving them motives. Swap out dungeon dressing for whatever is appropriate to the locations and environments. These will ultimately serve as physical clues and evidence, but don't think of them as that quite yet. They're just world details about the world. Sometimes the random placement is going to be logical. Sometimes it's going to be something awesome never thought of yourself. A lot of the times, it may seem odd or out of place. The idea here is to try to make sense of it. Just like players would have to try to make sense of it. This is actually what gives a huge feeling of mystery. As creator doing this in advance, your rationales about misplaced items actually become what happened. You may have to go back and do some curating. Something that blatantly points to what happened might be altered by the perpetrator. That thing having been eliminated but perhaps there being some clue or clues that the physical evidence has been altered in some way.
It's a little extra work up front to do the mindset shift. But once you've got it, you can pump out mystery adventures effortlessly. The flow of the adventure is generally going to be following up on leads. This is as opposed to the sort of mystery stories you might see in Columbo, where the detective usually has it figured out from the start and is just trying to get the perp out himself.