Unfortunately I have little to reproduce:
I have a custom build hexagonal grid with out-of-the-box cylinders on it. The camera is a TargetCamera. In 2.5 clicking on a cylinder picks it (using scene.pick) in the current preview release, it picks the hexagonal grid tile below. I stepped through the non-minified BabylonJS code a bit, and it seems it has nothing to do with isPickable, isVisible or isEnabled() - it is actually the intersection check that seems to have regressed: https://github.com/BabylonJS/Babylon.js/blob/master/src/babylon.scene.ts#L2872
Sorry for not providing a minimal test case. I have downgraded to 2.5 for now, but I thought you still might want to take a look, and maybe you already have a hunch of what might be causing it.
