It appears to mean 'We have not been smoking [in the last unspecified time frame]'.
The timeframe is derived from context.
'We have not been fighting!'.
From some children who's parents have just got home, probably means 'We have not been fighting this evening'.
'We have not been eating dairy'.
Would have a larger time frame, anywhere from a couple of weeks to a few months.
'We have not been smoking'.
It really depends on the context. At a cocktail party where the couple hasn't seen another couple for a while, they may mean that they've quit smoking and haven't smoked in a few weeks/months.
Whereas from a suspicious mother, it might mean that they haven't been smoking this evening.