I think it has to do with no refueling. The crucial (only) part of the pit stop is to change the tyres, so they try to do it as fast as possible, whilst before, they had more time (the fueling takes longer). Not sure if anything technical of big importance has changed, maybe only more advanced guns/methods. But the reason for the mistakes is the hurry in which they change the tyres, I think.
Wheel nuts were sometimes an issue back in the early 2000s and earlier, but it was generally with either cross-threading or midfielder teams fumbling – due, perhaps, to insufficient practise. Once the big teams demonstrated that sufficient practise could make a well-drilled team, the practise (pun intended) percolated down the field, reducing mistakes. Some teams at both ends of the field also found good ways of preventing cross-threading.
However, the combination of reduced stop time (to which LL Jehto alluded) and the increase in pit stops (to which Keith alluded) has reverted the situation. Since the two factors are independent of financial firepower, all teams are getting about equal effects from this.