Every government functions upon its bureaucracy.  By trying to do everything "in-house" Trump is making it more difficult for the bureaucracy to work with him, more likely to work against him, and putting an unnecessary amount of strain and stress on his administration resulting in shoddy, piece-meal products like the travel ban.  He seems intent on foolishly taking on the DC juggernaut single-handedly and blaming everyone else when he fails.
His inexperience is only compounded by his lack of temperament.  The worst part is that this isn't even the scary bit.  A falling out with the bureaucracy might leave some injuries that mostly can be band-aided over.  No, the scary bit is Trump's fumbling about in the international arena where ISIS recruitment gets empowered, any country basing its legitimacy on anti-US sentiment grows in authority and the more experienced players like Russia and China play him for a fool.