The problem is with soul trapping: It seems that a fair number of creatures have soul levels that are higher than they should be. I can kill mudcrabs, and I get common souls. I can't find any petty or lesser souls. (Maybe deer?, but I can't find any atm,) I'm level 15 in an FCOM game, in case that matters...
I'm not even sure what could cause this problem.
Spoiler
Active Mod Files:00 Oblivion.esm01 Francesco's Leveled Creatures-Items Mod.esm [Version 4.5bSI]02 Francesco's Optional New Items Add-On.esm [Version 4.5bSI]03 Cobl Main.esm [Version 1.73]04 Oscuro's_Oblivion_Overhaul.esm [Version 1.34]05 Mart's Monster Mod.esm [Version 3.7b3p3]06 Enhanced Daedric Invasion.esm07 TamrielTravellers.esm [Version 1.39c]08 FCOM_Convergence.esm [Version 0.9.9MB3]09 Armamentarium.esm [Version 1.35]0A Artifacts.esm [Version 1.1]0B Progress.esm [Version 2.2]0C Unofficial Oblivion Patch.esp [Version 3.3.1]0D DLCShiveringIsles.esp0E Unofficial Shivering Isles Patch.esp [Version 1.4.0]0F Francesco's Optional Chance of Stronger Bosses.esp10 Francesco's Optional Chance of Stronger Enemies.esp11 Francesco's Optional Chance of More Enemies.esp12 Francesco's Optional Leveled Guards.esp++ FCOM_Francescos.esp [Version 0.9.9]++ FCOM_FrancescosItemsAddOn.esp [Version 0.9.9]13 FCOM_FrancescosNamedBosses.esp [Version 0.9.9]++ Item interchange - Extraction.esp [Version 0.76]14 Display Stats.esp [Version 1.3]15 Enhanced Economy.esp [Version 5.0.1]16 Crowded Cities 15.esp17 Crowded Roads Advanced.esp [Version 1.3]18 Populated Prisons.esp19 FormID Finder4.esp1A Streamline 3.1.esp1B Map Marker Overhaul.esp [Version 3.7.1]1C Map Marker Overhaul - SI additions.esp [Version 3.5]1D DLCHorseArmor.esp1E DLCHorseArmor - Unofficial Patch.esp [Version 1.0.5]1F DLCOrrery.esp20 DLCOrrery - Unofficial Patch.esp [Version 1.0.3]21 DLCVileLair.esp22 DLCVileLair - Unofficial Patch.esp [Version 1.0.5]23 DLCMehrunesRazor.esp24 DLCMehrunesRazor - Unofficial Patch.esp [Version 1.0.4]25 DLCSpellTomes.esp++ DLCSpellTomes - Unofficial Patch.esp [Version 1.0.1]26 DLCThievesDen.esp27 DLCThievesDen - Unofficial Patch.esp [Version 1.0.5]28 DLCThievesDen - Unofficial Patch - SSSB.esp [Version 1.0.4]29 Cobl Glue.esp [Version 1.73]2A Cobl Si.esp [Version 1.63]2B Bob's Armory Oblivion.esp2C FCOM_BobsArmory.esp [Version 0.9.9]2D Loth's Blunt Weapons for Npcs.esp++ FCOM_LothsBluntWeapons.esp [Version 0.9.9]2E Oblivion WarCry EV.esp [Version 1.09]2F FCOM_WarCry.esp [Version 0.9.9MB5]30 Oscuro's_Oblivion_Overhaul.esp [Version 1.34]++ OMOBS.esp [Version 1.0]++ OMOBS_SI.esp [Version 1.0]++ ArmamentariumLLVendors.esp [Version 1.35]31 ArmamentariumArtifacts.esp [Version 1.35]32 OOO 1.32-Cobl.esp [Version 1.72]33 Mart's Monster Mod - Additional Enemy NPC Vars.esp [Version 3.7b3p3]34 FCOM_Convergence.esp [Version 0.9.9Mb3]++ FCOM_EntropicOrderRebalance.esp [Version 0.9.9beta2]35 FCOM_RealSwords.esp [Version 0.9.9]36 FCOM_DurabilityAndDamage.esp [Version 0.9.9]37 Mart's Monster Mod - More Wilderness Life.esp [Version 3.7b3p3]38 Mart's Monster Mod - Extra Wounding.esp [Version 3.7b3p3]++ Mart's Monster Mod - Looting NPCs & Creatures.esp [Version 3.7b3p3]++ Mart's Monster Mod - Less Bone Loot.esp [Version 3.7b3p3]39 Mart's Monster Mod - Dungeons of MMM.esp [Version 3.7b3p3]3A Mart's Monster Mod - Gems & Gem Dust.esp [Version 3.7b3p3]3B Mart's Monster Mod - Hunting & Crafting.esp [Version 3.7b3p3]3C Mart's Monster Mod - Farm Animals.esp [Version 3.7b3p3]3D Mart's Monster Mod - Diverse WaterLife.esp [Version 3.7b3p3f]++ Mart's Monster Mod - Slof Horses Complete.esp [Version 3.7b3p3]++ Mart's Monster Mod - Diverse Runeskulls Loot G&GD.esp [Version 3.7b3p3]++ TamrielTravellerAdvscript.esp [Version 1.39c]3E TamrielTravellers4OOO.esp [Version 1.39c]3F TamrielTravellersItemsCobl.esp [Version 1.39c]40 ShiveringIsleTravellers.esp [Version 1.39c]++ ShiveringIsleTravellersFriendlyFactions4MMM.esp [Version 1.39c]++ FCOM_DiverseGuardUnity.esp [Version 0.9.9]++ FCOM_BobsGuardUnity.esp [Version 0.9.9]++ FCOM_HungersUnitySI.esp [Version 0.9.9]++ FCOM_FriendlierFactions.esp [Version 0.9.9]41 FCOM_MoreRandomSpawns.esp [Version 0.9.9]42 FCOM_MoreRandomItems.esp [Version 0.9.9]++ Mart's Monster Mod - Shivering Isles.esp [Version 3.7b3p3]++ ArmamentariumLL4OOO.esp [Version 2.01]++ ArmamentariumLLMagicOOO.esp [Version 1.35]++ MMM-Cobl.esp [Version 1.73]43 ArmoryLab.esp44 Artifacts.esp [Version 1.1]++ Artifacts - ArmaCompleteAddon.esp [Version 1.0]45 DLCBattlehornCastle.esp46 DLCBattlehornCastle - Unofficial Patch.esp [Version 1.0.4]47 DLCFrostcrag.esp48 DLCFrostcrag - Unofficial Patch.esp [Version 1.0.4]49 Knights.esp4A Knights - Unofficial Patch.esp [Version 1.0.9]4B Mart's Monster Mod - City Defences.esp [Version 3.7b3p3]++ FCOM_Knights.esp [Version 0.9.9Mb3]4C Enhanced Daedric Invasion.esp4D Harvest [Flora].esp [Version 3.0.0]++ Harvest [Flora] - Shivering Isles.esp [Version 3.0.0]4E HUD Status Bars.esp [Version 1.2]4F Salmo the Baker, Cobl.esp [Version 3.08]50 Soulgem Magic.esp [Version 1.0]51 Enhanced Economy - House prices.esp [Version 1.0]52 Quest Award Leveling SI.esp53 Quest Award Leveller.esp++ Quest Award Leveller - Battlehorn Castle.esp++ Quest Award Leveller - Vile Lair.esp++ Quest Award Leveller - Mehrunes Razor.esp++ Quest Award Leveller - Knights of the Nine.esp54 RenGuardOverhaul.esp55 nGCD.esp56 ProgressMBSP.esp [Version 2.0]57 ProgressSBSP.esp [Version 1.0]58 ProgressRBSP.esp [Version 1.0]59 ProgressArmorer.esp [Version 1.0]++ Item interchange - Placement for FCOM.esp [Version 0.76]++ Item interchange - Option, Ingredients in Bulk, reduced.esp [Version 0.76]5A bgBalancingEVCore.esp [Version 10.52EV-D]5B bgMagicEV.esp [Version 1.7EV]++ bgMagicSpellTomes_for_WryeBash.esp [Version 1.68EV]++ bgMagicItemSigil.esp [Version 1.68EV]++ bgMagicEVStartspells.esp [Version 1.68EV]5C bgMagicBonus.esp [Version 1.7EV]++ bgMagicEVAddEnVar.esp [Version 1.68EV]5D bgMagicEVPaperChase.esp [Version 1.68EV]5E bgMagicAlchemy.esp [Version 1.57]5F bgMagicPotionNumberSoulGemValue.esp [Version 1.68UV]60 bgBalancingOptionalLessHealth.esp [Version 10.0UV-U]++ bgBalancingEVOptionalMoreEyes.esp [Version 10]** bgBalancingEVOptionalNPCDiversity, Beautification.esp [Version 10.0EV-D]++ bgBalancingEVOptionalFCOMAdditions.esp [Version 10.]61 bgMagicEVShader.esp [Version 1.7EV]++ bgMagicShaderLifeDetect.esp [Version 1.68]62 bgMagicLightningbolt.esp++ FCOM_Archery.esp [Version 0.9.9]++ Cobl Filter Late MERGE ONLY.esp [Version 1.53]63 Bashed Patch, 0.esp64 ChrisMOD.esp //This is a minor edit that changes the value of what a given level soul 's total enchantment value is, and the amount of charge a given level soul can use per use.