“Something (is) rotten in the cotton” is a Southern expression meaning that something is wrong. U.S. president Lyndon B. Johnson (1908-1973) is credited with saying it.
 
“Something rotten in the cotton” appears in print by at least 1961, when the line was used in the play Purlie Victorious by Ossie Davis.
 
     
Google Books
Purlie Victorious; a comedy in three acts
By Ossie Davis
New York, NY: Samuel French
1961
Pg. ?:
GITLOW. Something is rotten in the cotton
 
3 March 1977, Augusta (GA) Chronicle, “Posted hours in mills is defended,” pg. 10C, col. 1:
COLUMBIA (UPI)—Rep. Kay Patterson, defending a state law requiring the posting of employe work hours in textile mills, accused Labor Commissioner Edgar L. McGowan and the house Labor, Commerce and Industry Committee Wednesday of being promanagement.
(...)
“Something’s rotten in the cotton” if textile firms support the measure, he said.
 
23 November 1977, Florence (SC) Morning News, “Mitchell Wants Survey Answered,” pg. 11A, col. 3:
Rep. Theo W. Mitchell says he thinks some persons don’t want to answer the questions because there is “something rotten in the cotton and there must be something they want to hide from the public and the General Assembly.”
   
Google Books
The status of efforts to identify Persian Gulf War syndrome : hearings before the Subcommittee on Human Resources and Intergovernmental Relations of the Committee on Government Reform and Oversight, House of Representatives, One Hundred Fourth Congress, second session, March 11, 28; June 25; and September 19, 1996.
By United States. Congress. House. Committee on Government Reform and Oversight. Subcommittee on Human Resources and Intergovernmental Relations.
Washington, DC: U.S. Government Printing Office
1997
Pg. 356:
Mr. TOWNS. Lyndon Johnson would say there is something rotten in the cotton.
   
Blogging Black Miami
Wednesday, May 16, 2007
Something is rotten in the cotton
JESCA (James E. Scott Community Association) is Miami’s oldest social service organization run by blacks. Most of its board of directors are prominent members in Miami’s black community. So why, pray tell, does Joe Arriola, a white Hispanic, need to bail out the organization?
     
MidlandsConnect.com
Missing person’s case becomes murder trial
By Crystal Walker
Tuesday, April 15, 2008 at 8:33 p.m.
(...)
Defense attorney I.S. Leevy Johnson says the State has not made its case and then reminds jurors about reasonable doubt. “Something just ain’t right, there’s something rotten in the cotton, now that’s what reasonable doubt is.” Johnson says this is not a murder case, “We contend this is a missing person’s case.”
 
New York (NY) Post
BofA’s counsel had no ‘legal’ authority in Merrill deal
By MARK DeCAMBRE, RICH WILNER and KAJA WHITEHOUSE
Posted: 1:00 AM, November 4, 2009
(...)
“This is another fact that leads me to believe there could be something rotten in the cotton,” Ed Towns (D-Brooklyn), chairman of the Congressional Oversight Committee, told The Post. He is investigating the BofA/Merrill merger.