2016 Formigal, 91 riders (55,4% the race péloton at that point) missed the time cut by a huge margin. They were 54 minutes behind on a stage which took 2h 54 minutes for the leaders to complete, 31% outside the winner's time - a level that would see you cut from most time trials. That group included people who've top 10ed many a Grand Tour, like Robert Gesink, Tejay van Garderen, Leopold König and Pello Bilbao. The issue is, once the gruppetto is big enough, they know they're safe and won't get bounced from the race, so they don't need to work hard. Only occasionally (one time in Tirreno-Adriatico in the 90s, for example) will the organisers go hard on the autobus when they're deemed not to have respected the race. The problem is the penalties, if the riders aren't thrown out of the race, only impact a small number of riders (those contesting the points classification) since a time penalty means nothing to guys already missing time cuts, and points penalties only impacts those who are contesting the points classification - and ironically, the guys contesting the points classification are probably the guys trying hardest in that gruppetto to honour the race anyway.
The Giro has been getting increasingly generous with their time cuts, but then they've often presented longer and harder stages and are at a time of year which means a higher risk of bad weather.