After the ability to transform, the second power Danny loses control over is intangibility. Yet later, he is seen phasing through the ceiling to confront Amorpho while the latter is disguised in Lancer's body.
When Danny's parents enter Casper High (literally destroying an entrance), they say "Freeze Fenton!" instead of "Freeze Phantom!" It isn't clear whether they were talking to Sam disguised as Danny Fenton or Danny Phantom.