Michael,
For me, yes it is common. I let the MMR team know about this last year, and they have not been able to come up with a solution.
I find that if my courses are in the area of where 4 satellite images are joined, the variance is the greatest. Since the satellite images are "rubber-sheeted", they stretch different amounts, based on the original images.
Also, I find that 5k courses can be just as far off as (or further than) half-marathon and marathon courses. I normally will map a course, then let the race director know that we need to allow for up to 100 yards of flex in the Start or Finish point, depending on their needs. If there is a spur, this is rarely an issue, but if they don't want a spur, but want the Start and Finish to be "really close to" certain points, it can pose a challenge.
You are not alone in your observation.