The app requires a code to record a test result, but a code is only received if the test is positive.
Those who claim they have symptoms without entering a result find that a countdown to self-isolation begins.
The Department of Health and Social Care said the app will be updated.
People who have used the app since its launch on Thursday and who had already booked tests before downloading it, found that they are unable to stop the self-isolation countdown after reporting symptoms if they get a negative result. because it does not come with a code that they can share.
"It's so confusing that the app doesn't tell you you can't enter booked negative tests outside of it," said Prof Deborah Ryan, who originally contacted the BBC.
"And the app still tells you to quarantine if you've entered symptoms. So does this mean I can't turn off the self-isolation alarm in the app?"
The self-isolation alarm cannot be turned off in this situation.
Furthermore, tests carried out following surveys by the Office for National Statistics and those carried out in a laboratory of the NHS Hospital or Public Health England, cannot be shared on the app regardless of the result
according to a tweet from the app's official account.
It is not clear how many test results would be affected.
The Department of Health said using the app is "entirely voluntary" and that the advice to take a test or self-isolate cannot be enforced.
Tests booked through the app will have the results automatically shared with it, he said.
According to data analyst App Annie, the NHS Covid-19 app has been downloaded about 4 million times so far.
"By downloading this app you are helping to protect yourself and others. If you book your test through the app, the results will be automatically recorded in the app and the isolation countdown will be updated," said a spokesperson for the DHSC.