Bryant made the comments on Friday during a forum discussion at the Cubs' annual fan convention.
"Who would want to play in St. Louis?" Bryant said "So boring. It's so boring. I always get asked like, 'Where do you like to play? Where do you not like to play?' St. Louis is on the list where I don't like to play."
Former Cubs pitcher Ryan Dempster backed up the third baseman.
"I'm like, 'Zero chance in hell. No way. Won't even go there as a free agent. Not happening," Dempster said.
Molina took to Instagram on Saturday, posting photos of Bryant and Dempster before calling them out in the caption.
"All-Stars, elite players and leaders of their teams do not speak bad about any city," Molina said. "There should be respect and you should play and compete with respect ... only stupid players and losers make comments like the ones made by Bryant and Dempster."
Molina also hashtagged "zero respect for these stupid players." He responded to several fan comments on the post with laughing emojis.
Bryant, 27, has played his entire career with the Cubs. The 2016 National League MVP avoided arbitration with a $12.9 million pact this offseason but is eligible for arbitration again next offseason.
His most recent comments came after Bryant attended a Florida Georgia Line and Nelly concert in December with his friend and free agent big fish Bryce Harper. Nelly -- a St. Louis native -- attempted to recruit Harper to the Cardinals while at the show.