Here's two instances that occurred in new base classes (@lukaspie and @mkuehbach):
NXcomponent contains NXfabrication which clashes with fabrication in subclass NXfresnel_zone_plate
NXapm_ranging (and also its NXprocess subgroups) and NXapm_reconstruction contain unnamed NXprogram groups but NXprocess has a program
Strictly, this is not a name collision though it can cause issues with autogenerated code and validators so it seems that perhaps
NXfresnel_zone_plate could name its fabrication field to something more descriptive
NXprocess could contain an NXprogram group or, conversely, NXapm_ranging and NXapm_reconstruction could specify named NXprogram groups