Why would a doctor question a neurological finding of epilepsy?

Many reasons: There are many mimics of epilepsy. Other examples of episodic neurological dysfunction include tia, migraine, or non-epileptic seizures. While MRI and eeg can be normal in people with epilepsy, it might make someone question the diagnosis. Other possible "red flags" might include specific aspects of the patient's history, and poor response to anti-seizure medications.

Many things: As an expert in diagnosing and treating epilepsy, many times i've had to "undiagnose" a person from epilepsy. It all depends upon the circumstances involved.