How did you measure the border? Did you measure across the center of the top to get the correct length? This has happened to me when I did not use the correct border length. It can also happen when the top is not flattened out fully on the batting. (The trick is NOT to stretch but pat it down flat. Hard to describe)
When it has happened to me, I simply accepted the "kisses" in the corner and went on to the next line. Once washed, the puckers tend to blend in a bit more.