^^Ahh, but they didn't warp back, they recreated the Borg's time vortex. And as we know from ENT, the Vulcan Science Directorate of that era regarded time travel to be impossible. So they wouldn't have recognized the vortex signature for what it was. At most, it would've been an anomalous, unexplained radiation surge.
As for the escape pods, there must have been a gap of several hours between the climax of the film and the arrival of the Vulcans -- not only because it would've taken time to get the Phoenix and Cochrane back to Earth, but because it was daytime when the Phoenix launched and night when the Vulcans arrived. So the E-E would've had hours to beam the escape pods back aboard before the Vulcans were close enough to detect anything. (And apparently Vulcans didn't have transporters back then, so again they wouldn't have recognized the energy signature even if they did detect it.)