The idea that sexual preference is a matter of biology, and not choice, has become more prevalent throughout the years. Sexual identity science consensus has followed suit. But like homosexuality in the past, an individual being uncomfortable with their original gender is often regarded as a mental illness.
But top authorities in the mental health community have debunked this, citing a few reasons.
The fifth edition on the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), published by the American Psychiatric Association explained that mental disorders are something that you want to treat against. But in the unique situation of someone questioning their sexual identity, science shows that not going through with a transition can sometimes have adverse mental effects on the patient. Therefore, the American Psychiatric Association chooses to label the condition not as a gender "disorder" but as gender "dysphoria"
Another reason why the American Psychiatric Association doesn't classify gender confusion as a disorder, is because the definition of a disorder is a psychological state that causes significant stress and disability. But in many cases, gender dysphoria is prevalent in mild doses, without a significant stress or disability presented. Therefore, it can't always fall under "disorder."
So we shouldn't really be calling gender identity confusion as a disorder. Transgender people aren't sick, and the dysphoria doesn't have the same attributes that would normally come with a disorder. Some cases are even temporary. But no matter what, transgender people need to be treated with respect just like everyone else, and that starts with recognizing what's actually going on.