Cross section of ceramic capacitors
It looks to me like the grinding/polishing has been done fairly well (with more care you could have less scratches), and you're looking at an accurate and undamaged image of the capacitor cross section.

The "dark" images are more or less what I'd expect to see from a capacitor cut across the planes of the electrodes.  Metal electrodes in a darker ceramic matrix.  For lower value capacitors I'd expect to see thicker parallel lines, but for the lines to be slightly wavy and broken isn't a huge surprise.  I expect that this results from the special steps they've taken to get the very high capacitance in a tiny package. Possibly a combination of grid electrodes rather than planes, and squashing/forming the ceramic after building the layers but before final firing in order to get the layers thinner.

The "pale" images are more or less what I'd expect for a capacitor sectioned parallel to the electrode planes.  Assuming you've used a metallographic grinder (looks like it) then your section plane is flat, but the electrodes aren't.  So you get contour-like features where the electrode crosses the section plane.

I doubt you'll find your leakage in these images. Other places to look:


Check the datasheets for the expected resistance.  Is it as high as you thought?  Check the conditions under which it is given in the datasheet, see if your environment is likely to make it worse.
Check a batch of new capacitors to see what the resistances are
Check a bunch of capacitors from your warranty returns to see if the capacitance or resistance has changed.
Measure the resistances on your PCB before assembly (should be nice and high)
Measure the resistance on a completed PCB (maybe sans MCU).  Look for evidence of flux which has not been cleaned well enough and could reduce the resistance.