Since when has the Doctor had trouble telling humans they are special/unique/have potential? 

Since Moffat made him into BBC Sherlock, that’s when. 

“You’re not special. You’re not important"—Tenth Doctor to Donna Noble.

*gif of Ninth Doctor consigning Adam Mitchell to a life of misery for not being special enough*

Remember when One nearly threw Ian and Barbara into the time vortex, even after they helped saved his life, in The Edge of Destruction?

“Don’t waste my time.” -the Tenth Doctor to a young woman who appears to be about to have a panic attack