It's really difficult to homogenize a mash by stirring. So, its not too surprising that the pH differs a bit through the mash. Its easier to homogenize the mash and wort by circulating it through the mash.
With that said, I wouldn't worry too much that your pH differed. Assuming that the water adjustments were made in pursuit of a proper pH, I wouldn't worry that a measurement differed from that target. But the measurements are helpful in guiding adjustments for future brews.
I take my first pH measurements at about the 15 minute mark since pH is changing via the variety of reactions and processes that are underway in a mash. I find that pH often continues to change as the mash duration increases. Don't worry that pH isn't perfectly on target, but hopefully its close.