I ran a smaller murder mystery recently, which had a specific end (to prevent further murders and schemes motivating these murder[s]), but was also used as a vehicle for introducing some more potential threads, npcs, and intrigue/flavor to the general story/campaign world, so the actual "murder mystery" itself is not the most developed.

Without nearly as many potential factors, complications, or nuances that a worthy logic puzzle could include, I basically set up a logic puzzle chart with the suspects (both known, and to be discovered), potential motives, and discoveries/clues, and PC actions discovered them or connected them.

My murder mystery was pretty simple in scale: a militia leader's closest guards/cohorts, a group of 4 npcs, are suspect in the murder of the leader's closest confidant/consult outside of their ranks, and a couple of other serious crimes/disruptions in the leader's plans. This is assumed because they are the only other people who are, to varying degrees, "in" the leader's circle and present/involved in his day-to-day affairs. The PCs, having already proven their worth to this leader and their ability to handle sensitive information on a previous task, are the only people nearby he feels he can trust to investigate this matter before it escalates. He shares information he knows about the four of them, information about the crimes that took place, and the PCs trailed/interrogated for more information, which led to other points/consequences.

There are more specifics (and I could detail them if anyone was interested), but that was the general frame I used, and from there I fleshed it out. In the setting of my game, the city they were in is split in two due to war/invasion with an outside faction. There were elements of betrayal/spying orchestrated from the opposing faction, but also general unrest from within as well due to morale/losses (both actual or perceived), which muddied the waters a bit for the PCs (in a good way). I also ended up including a simple cipher puzzled message they intercepted where they could either attempt it themselves or rely on an NPC to do it, with the caveat that it would take time and with events playing out the longer it took the more threats and negative events occurred or had to be managed).

This was run at a lower level (3rd lvl characters, I think), but I was pleasantly surprised by some of the creativity of my players. Just expect surprises and get ready to roll with them.