The Issue with Enemies ignoring staggers seems to origin frequently on ledges, jumps, falls where enemies get staggered but the climbing/jumping-state prevents staggers to have an effect.
It further seems to be possible that the applied effect looses it’s expiration timer while beeing ‘prevented’ and now blocks the possibility to apply a stagger which is equal or weaker than the firstly applied stagger effect. (This also may be a good opportunity to look if prevented staggers get properly deleted during missions, which may not be the case 
)
This would experience several occasions i experienced where units became unstaggerable after climbing/jumping until their death.