The latest version of Prodigy isn't officially compatible with spaCy v2.2 – so this is likely the problem here. spaCy v2.2 introduces stricter and backwards-incompatible behaviour around overlapping entities.
We will be releasing an officially compatible version of Prodigy soon – we typically wait until the latest version is confirmed stable and any remaining bugs (library and pre-trained models) are resolved. (Otherwise it'd be irresponsible to tell Prodigy users to upgrade and retrain all their models.)