Mine does it doesn't really bother me. He is a 8 month old German Shepherd and he's very armttached to people so whenever they leave he cries a lot and looks out the window all night, he cries if my kitty is being mean to him, he cries when he has to go potty. Is your dog the same way? Maybe...
I've noticed that when I am walking him and we pass by another dog that might bark he whines like if he is scared of him. But he still wants to go up to the dog and smell him and if the dog gets very aggressive and keeps barking then he will bark back.
I really don't understand if he is scared...