Benson and cornerback Adam "Pacman" Jones are subject to league discipline for arrests that occurred during the NFL's lockout. Eight players overall are facing discipline under the league's conduct policy. Benson has a hearing scheduled for Tuesday.
Whitworth said Monday he wouldn't have supported the new collective bargaining agreement if he knew players would be suspended for things that happened before the deal was reached.
"I was very shocked," Whitworth said. "It doesn't make a whole lot of sense to me.
"I feel like it's the wrong decision, and I also believe the union let those eight guys down. I don't feel like that was fair. To me, if I was told that was a make-or-break, I would have said that's a make-or-break deal, that we were going to sell out eight guys to have an agreement."
When the deal was reached in July, it was unclear whether the league could fine or suspend players who got in trouble during the NFL's 4½-month lockout, when there was no collective bargaining agreement. The NFL Players Association had decertified as part of the labor dispute.
The league and the NFLPA eventually agreed that eight players could be disciplined for incidents in the offseason, while 25 others would not be.
"I feel like it was the wrong decision to allow those guys to be punished," Whitworth said. "They weren't employed (during the lockout) and they didn't have a job, so they shouldn't be able to be punished for it.
"Now, I don't think that them doing stuff is OK. But if no one else can get punished, they shouldn't be able to, either."
A source confirmed to ESPN senior NFL analyst Chris Mortensen on Sunday that Benson has filed an unfair labor practice charge against the NFLPA with the National Labor Relations Board regarding the agreement and citing the decertification.
Among his arguments, Benson claims that since the NFLPA wasn't a union after decertifying during the lockout it had no right to make an agreement with the league on players who could be disciplined.
Benson, speaking after the Bengals' 13-8 loss on Sunday, was none-too-pleased with his union officials.
"There were some things in the CBA that we were not made aware of, which is really no surprise," Benson told The Associated Press. "That kind of falls on the (players' association). You would think they're here to support you and have your back -- that's what a union does. I guess in my case, it's different."
Benson was arrested during the summer of 2010 over an alleged bar fight in Austin, Texas. He was charged with misdemeanor assault. Benson met with NFL commissioner Roger Goodell after the incident and wasn't disciplined. He was arrested again last July and charged with misdemeanor assault over an altercation with a former roommate in Austin.
Benson reached a plea agreement to settle both court cases and served five days in a Texas jail before the season began.
Jones faces trial in November over his arrest at a Cincinnati bar last July on misdemeanor charges. The case is being monitored by authorities in Las Vegas, where Jones is on probation from a 2007 strip club fracas. Jones has repeatedly been in trouble during his NFL career.
Information from The Associated Press contributed to this report.