Take a methodical approach. First, look at the board bond pads. Board shops often (too often) make changes in the design and do not communicate this to the end customer. Ensure that the spacing between bond pads is uniform throughout under the BGA
Next, take a look at the BGA. Is the spacing between the balls uniform? Deliberate changes (such as an array that is not fully populated) or unintended changes could drive this behavior.
Finally, do the same thing with your stencil pattern.
If everything looks good, then I would start to suspect out of plane deformation of the BGA (aka, potato chipping) during the reflow process.