I felt like I had the same issue. I have a mesh of 23x19 points, always taken after at least an hour of heat soak in. I do this for each one is my removable print plates.
I have an extremely flat build surface underneath and I even go so far as to manually probe the bed at randomly chosen probe points to validate the mesh.
The tested points always nearly exactly match the saved mesh.
But when I print, there is always one area, on each of my 6 different plates that acts like a low spot.
All I could think of was that my kinematics were out of whack somewhere so the reasonably large offset between the probe and my tool must be revealing that.
Maybe you have the same issue? I have a tool changer, that's why my probe is so far away.
BTW, I fixed it by squaring my frame, checking all along the lengths of the body and added braces where they were the wrong distance apart.