I don't know if this is normal, or when it took effect, but I didn't notice anything wrong when in Seyda Neen. All the alchemy ingredients I found in containers were from the Morrowind set. However, once I got to Balmora, I installed some menu and interface mods, which I didn't think would have any effect on vendor lists. When I looked at the store inventories of the various alchemy vendors, like Nalcarya of White Haven or Sharn gra-Muzgob (of the Mages Guild) they only sold Oblivion ingredients, with the exception of small kwama egg.
My load order looks like this:
GameMode=Oblivion
Oblivion.esm=1
Morrowind_ob.esm=1
Unofficial Oblivion Patch.esp=1
UOP Vampire Aging & Face Fix.esp=1
Oblivion Citadel Door Fix.esp=1
DLCBattlehornCastle.esp=1
DLCShiveringIsles.esp=1
DLCBattlehornCastle - Unofficial Patch.esp=1
Unofficial Shivering Isles Patch.esp=1
DLCThievesDen.esp=1
DLCThievesDen - Unofficial Patch.esp=1
DLCThievesDen - Unofficial Patch - SSSB.esp=1
DLCMehrunesRazor.esp=1
DLCMehrunesRazor - Unofficial Patch.esp=1
DLCVileLair.esp=1
DLCVileLair - Unofficial Patch.esp=1
DLCHorseArmor.esp=1
DLCHorseArmor - Unofficial Patch.esp=1
DLCOrrery.esp=1
DLCOrrery - Unofficial Patch.esp=1
DLCSpellTomes.esp=1
DLCSpellTomes - Unofficial Patch.esp=1
DLCFrostcrag.esp=1
DLCFrostcrag - Unofficial Patch.esp=1
Knights.esp=1
Knights - Unofficial Patch.esp=1
Morrowind_ob - MorroblivionTreeReplacer.esp=1
Morrowind_ob - UCWUS.esp=1
Morrowind_ob - Conversation.esp=1
Harvest Nearby Flora.esp=1
Morroblivion - Buyable Houses.esp=1
Morrowind_ob - Chargen and Transport Mod.esp=1
Morrowind_ob.esp=1
MorroblivionNewMap.esp=1
Morrowind_ob - Morroblivion Maps.esp=1
QZ Easy Menus.esp=1
Retroactive Health.esp=1
Bashed Patch, 0.esp=1
Ajira in the Mages Guild has
Ajira in the Mages Guild has 65 in her Shopping list. Try Deactivating what you put on before you went to Balmora.Could also be todo with your Alchemy Level.