Hello!
I think you should check the pixel values in the overlapping area. Sometimes the the images appear with different brightness and contrast depending on the contrast strech applied by the software you are using to visualize them, even though they might have the same pixel values.
If your pixel values are, indeed, different, then you have the same problem as me and I hope somebody can fix it!
The thing with the Sen2Cor process is that each tile is processed separately, and the calculations for the atmospheric correction are done based on the values of each tile. They have an overlap, but the tiles themselves are different. Consequently, the calculations are different for each one.
Sorry I don’t have a solution!