"It's one that we're still scratching our head on," Hoyer said.
On Tuesday, Hoyer told MLB.com and XX 1090 AM, the Padres' flagship station, that the team reached an agreement with Whitson, the ninth-overall pick, for $1.953 million on the day of the Draft.
The Padres initially had slotted Whitson at between $1.9 million and $2 million, as per the recommendation of Major League Baseball.
"Somewhere along the way, over the next couple of weeks, I don't know who got in his ear, but he completely changed his tune from being thrilled to being a Padres and having that verbal agreement to us having to double that amount to sign," said Hoyer, who said conversations with the Whitson family before the Draft were never centered on money.
"Things got a little rocky. We held firm ... that we had a verbal agreement. We thought they would come back and honor that word."
When Oakland signed outfielder Michael Choice, the No. 10 overall pick to a $2 million on July 28, the Padres increased their offer to $2.05 million. They made another offer, this time of $2.1 million to get closer, as Hoyer said, to what the eighth overall pick got.
Houston signed Delino DeShields Jr., the eighth overall pick, to $2.15 million.
"He [Whitson] wanted to get paid like the No. 4 or 5 pick in the country and wouldn't lower it," Hoyer said. "I'm shocked. We had a deal with this kid. Somewhere along the line, someone told him he was worth more."
An e-mail to Whitson's advisor, Troy Caradonna of SFX Baseball, wasn't immediately returned Tuesday.
San Diego owner Jeff Moorad, a former agent himself, said he was disappointed that the first number presented to the team by Caradonna was just 15 minutes before the deadline and was $2.7 million, and that he felt sorry for Whitson in the end.
"Naturally, we're disappointed," Moorad said. "To hear that the player was "crushed" after the deadline passed tells us that this was agenting gone bad at it's best. ... If we're committed to anything, it's to carry ourselves professionally and do business in the right way."
Whitson, who had signed a letter of intent to pitch for the University of Florida, will presumably go that route and will be eligible for the Draft following his third season, unless he enrolls at a junior college.
The Padres will receive the No. 11 overall pick in the first round of the 2011 First-Year Player Draft in addition to their own pick, which will be contingent on where they finish the regular season.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.