My gut tells me the polishing oils were not removed prior to waxing, then wound up inadvertently mixing with the wax when it was being applied. That said, it also cannot be confirmed the holograms were removed after polishing since the oils would mask the 'grams as well.
If the holograms are due to product reasons, then apply some QD to the panels, wipe with some pressure and that should help. Over time the holograms will disappear as the LSP fades away. Another approach would be to do a 50/50 on a panel - one side leave alone or QD it. The other side, wash, clay lightly and quickly, QD, IPA, then apply wax. Compare both sides for holograms. If your fully treated side still shows holograms then it was your polishing process and/or technique that needs some fine tuning before you re-polish the whole car.