Since it is a glass substrate you are taking about, I would suppose what you see ist a charging effect at the Interface. I also have already observe such darker zones below the coating in a glass substrates.
good point... I always assumed SE-imaging using ions :-(. Hayk, did you used the electron beam for the imaging or the ion beam (collecting the generated SE signal)?
I also think it is a charging phenomenon. I have observed a similar thing in a thin-film silicon solar cell. See the attached image. On the left with SE detector you clearly see a darker region in the glass below the TCO. With the BSE detector is is not visible. It is also not an effect of the FIB polishing, because I also see it in cleaved samples without any FIB polishing.