Sure, someone may have noticed it, if he were just some lowly American peon waiting in the Customs & Immigration line, but he's a bigtime VIP US Senator. Those people go through the diplomatic express line, and are never given anything but scant scrutiny.
I highly doubt that any immigration agent ever gave his US passport anything more than a cursory glance before stamping it.
And Obama would have had to show his Passport to officials in other nations.
Moreover, the people who breached his Passport file would have noticed that his place of birth was Kenya.