Wiki wrote:
* Do not cast the soultrap spell on two different beings (or twice on the same being) within the 120 second time-frame of the spell. This will cause the spell to stop functioning correctly on all future casts regardless of whether you kill the NPCs that you double-cast on or not.
o On the PC, a fixing mod can be downloaded (Hermaeus Mora Daedric Quest Fix).
o PC Only This bug is fixed by the Unofficial Oblivion Patch.
o A workaround is possible on PC, Xbox 360, and PS3. Cast the soul trap on an unwanted NPC and then cast it again (within 120 seconds) on the NPC you actually want to trap (at this point, if everything was well a pop-up message would appear telling you that you can only soul trap one person at a time). Now kill the second NPC and you should trap their soul successfully (assuming you needed their soul in the first place!). If this does not work, cast the spell on an invalid target (e.g. a crate, barrel, horse) and then on your desired target. All ten races can be collected this way, without having to revert to an older save.
o Another possible workaround on Xbox 360 is to cast the soul trap on an unwanted NPC only once, then twice on the desired NPC. If you receive the message stating Mora's Soul Trap is already active after the second cast on the desired NPC, you can kill that NPC and capture its soul. This method requires that two NPCs be present to capture any soul.
* Occasionally you will not be able to soul trap one of the races.
o Saving your game to a new save (be sure to not overwrite the last save made before the start of the quest), quitting out of the game entirely, restarting, and reloading can fix this problem.
o Another method is possible. Cast Hermaeus Mora's Soul Trap spell on an NPC two times within 120 seconds, and within the same time period, cast the spell again on the NPC you wish to capture. You will not get a message stating that you "You cannot cast this spell on multiple targets", but the 2nd NPC is now able to be trapped.
o If saving and reloading does not work then you may have to load a game that was saved prior to the start of Hermaeus Mora quest and redo the quest.
o On the PC, you can use console commands to bypass the rest of the quest. The command player.setstage 000146AF 40 gives you automatic credit for capturing all 10 souls.