Like Naruto was aware of the Pein that was just resurected? When the plot needs people to don't sense then they don't sense.
How about Naruto detecting the ENTIRE BATTLEFIELD with people and enemies he NEVER got to see again by just exiting the cave but he could not sense Nagato and Konan that where just outside Konoha and he had to stab himself... Seriously?
Also Naruto showed those senses in his fight with Pein only when traking him down. Aside from that... Not that much...
Then yes Naruto did say he can feel the entire Konoha now that he has senjutsu chakra in him and made it look like that is a normal ability shared by all. Even Ma/Pa should have it.. Hell Ma senses Pein when they got there in all that dust. Then of coruse not even Ma/Pa could sense the 3 sneaking Pein...
Well what else could it be? Are you telling me the elder frogs themselfs don't have special senses?
Seriously they never showed it as they did not really need to show it. Aside from detecting where Nagato is Naruto did NOT display any SM senses in his fight with Pein... If not for that we would asume (just like with JMan) that he does not have it (aside from looking for Kakashi something that JMan would obviously have no need to do in his fight with Pein)....
Senjutsu chakra works by activating your body, all of it, senses including.
Read what Naruto states here:
http://www.narutobase.net/manga/Naruto/431/3
Now that he has naure energy... Do you see him stating how he is the only one who can do that? That Ma, Pa, JMan could not do it or how he was a special case? I men ANYTHING?
No he just trows that line like its a NORMAL ability for all after they got senjutsu chakra.
And again here Pa is speaking generaly about the sage mode ability:
http://www.narutobase.net/manga/Naruto/431/17
Later with Kabuto when dodging that arrow he AGAIN states it generaly like its nature working with him...
I can understand JMan perhaps not having it on the same level but not having it like at all? Now that is absurd. If Naruto showes the ability to kill Pein with a Rasengan then JMan can do the same. Its just about same thing with SM.