Genuine Lonely

New experiences in our family are often, but subtle.  Last night we had one that was a bit more significant. 

The girls had gone to bed later than the late time we generally account for.  About 20 minutes later however, Caitin opened the door and after enduring some barking from Mom and Dad asked, "Mom, how come you and Dad stay up really really really really really really late?"
She seemed to want to talk, but Sarah sent her back to bed.  We were nearly ready to go to bed ourselves at this point, when Caitin began crying from her bed.  This was not the 'I don't want to go to bed and I'm mad about it!'-cry, but rather the 'I'm sad and hurt'-genuine-cry.  Sarah must have sensed the difference as she went in to talk to her.  "What's wrong, Caitin?" she consoled.
"I'm sad and lonely!" Caitin sobbed.
"But you don't have to be lonely, we're right here." Sarah stated.  Caitin continued to cry and Moan.  "We're right outside your door.  There's no reason to be lonely."  Sarah reaffirmed.
Stifeling her tears, Caitin blurted, "Can you get my bear so I won't be lonely?"
Sarah obliged.  I believe there was a hug associated with the final goodnight before Sarah left the room.  Her tears stopped, but the occasional sobs lingered for a few moments until she was calmed.  I couldn't help but go in and get one of those genuine lonely hugs too.

The significance of this experience was in that genuine cry as an expression of lonliness.  At what point do feelings become tied to external stimuli as opposed to simple child-like instinct?  Or are they always tied, and only occasionally seem so clearly affected one way or the other?