I had some trouble getting Prodigy working with my JupyterLab and in the end I just tried every solution on the web repeatedly until it eventually it "works" ( I say works in inverted commas as the trouble installing it makes me anxious and no idea what got it going).
I then ran the NER fully manual annotation example with the news headlines download
Sorry to hear you had troubles installing Prodigy! I wonder what the issue was, because I just had to do the fresh installation to check your issue and it worked almost seamlessly. I do admit that our docs instruct to use a deprecated way of installing a jupyter plugin that will lead to an error. The error message does say that you should use pip instead.
Let me just recount the steps in case someone else stumbles upon a similar issue
with these steps you should be able to run Prodigy in jupyter.
Back to your question, by labels are the same you mean that PERSON,ORG,PRODUCT,LOCATION appear in the UI?
Not really sure why you could possible see such behavior. Could you re-run your command with a fresh target dataset!python -m prodigy ner.manual ner_animal_data_test blank:en ./animal.jsonl --label CAT,DOG,FOX command and send me a screenshot similar to this one: