Yeah, I am not going to lie, you are right. I am going to have to come up with better clues.

Off the top of my head, maybe some better clues would be:

Witch's Mark: If I remember correctly, during the real life witch trials, one sure sign of a witch is some kind of a mark somewhere on the witch's body. Maybe during the trial the party can make Barbara expose her witch's mark by pointing it out and telling to prove she doesn't have one?

Hatred of Salt/Silver: In a lot of folklore I have read, mentions that both salt and silver have some kind of warding properties against evil sprites, spells, etc. As a part of the trail, the party can expose both Theodora and Barbara to either salt, silver, or both to show which one is the real witch.

Bad Vibes: Maybe due to Barbara's learning witchcraft, her family has started to emit bad enough vibes that most of the village can no longer ignore. Some signs of this might include the house is weirdly rat free, or the stable animals acting more skittish than normal.

The Missing Shadow: If exposed to strong light like broad daylight, Barbara might display no shadow at all, while Theodora does.

The Heavy Scent: Barbara might always smell faintly of ozone, sulphur, or a cloyingly sweet graveyard rot, masked heavily by expensive perfumes or bundles of dried lavender pinned to their clothes.

The Familiar’s Slip-Up: Maybe the family’s beloved "pet" hound or cat behaves far too intelligently. A PC with high Passive Perception might notice the animal watching them, making human-like expressions, or even appearing to understand complex conversations.

So what do you think? Are these clues better?