Correa, 28, sent shockwaves through the league when he agreed to a 13-year free agent deal with the Giants, only for the signing to be called off three hours before the scheduled introductory press conference.
With San Francisco off the table, Correa and agent Scott Boras moved on to the New York Mets, agreeing to a 12-year, $315m contract – which has still not been finalised as they tackle the same medical issues that scared away the Giants.
In his first interview since the debacle, Zaidi made an effort to insist those risks are simply a part of the free agent game.
"I was on the phone with Scott Boras on the Monday that we did Carlos' physical right when his plane landed," he said. "So any suggestion that this was an 11th-hour thing is just not accurate.
"As soon as we had information, we shared it. We have a good working relationship with Scott Boras and his agency."
Zaidi confirmed the Giants and Correa's camp had "a difference of opinion on the medical review" – with ESPN's reporting adding that it is regarding an ankle injury and subsequent surgery on the issue back in 2014.
The Giants were also considered the favourites to land the top free agent on the market, but reigning American League MVP Aaron Judge shunned them to return to the New York Yankees on a nine-year, $360m deal.
As a result, Zaidi himself became a target online of disgruntled Giants fans, and he admitted that is hard to get use to.
"It's always a little jarring when you open up your Twitter app just to see what's happening in the world and your name is trending," he said. "That's generally not a good thing.
"At the end of the day I understand it comes with the territory. We have fans that really care, really are invested in this team and at the end of the day our job is to just put a compelling, fun team to watch on the field.
"This is baseball, I feel really fortunate to be in this job, I love it. I love the responsibility that comes with it, and part of my responsibility when things don't go your way is to support and lift other people up and not dwell on the negatives."
The Giants ended up addressing their outfield need with former Seattle Mariner Mitch Haniger on a three-year, $43.5m deal, as well as New York Mets left-handed bat Michael Conforto for two years and $36m.