Riders sat out more than half of Friday's planned 258km race from Morbegno to Asti after concerns were raised over racing in heavy rain.
Giro organisers agreed with the Professional Cyclist's Association to start the days racing 124km from the finish.
Czech rider Josef Cerny of CCC won the stage, while Sunweb's Australian rider Jai Hindley moved to within 12 seconds of GC leader and teammate Wilco Kelderman.
In an interview with Eurosport, Vegni said he was disappointed with how the situation was handled by the riders.
"[I'm] very upset about the way it's happened. It isn't the right way to resolve these issues," he said.
"I think there are going to be words with lawyers - I don't think it's respectful to the race or people who want to watch.
"Today the parcours [course] was lovely. There will be consequences because of the behaviour of the riders."
Many riders revealed they feared competing in the heavy rain would increase their risk of contracting coronavirus.
It wasn't about the weather conditions," EF Pro Cycling's Simon Clarke said after the stage.
"It was about the distance and how hard this week's been. It just seemed unnecessary to race 260 plus kilometres of flat, so we tried to find a compromise whereby we could race and put on a spectacle, but not race unnecessarily long distances."