The ex-Borussia Dortmund pair have both been linked with moves away from the Allianz Arena but, while Gotze - a reported target for Liverpool - is said to have been urged to leave by club officials, Bayern appear determined to keep Lewandowski.
This stance contrasts that of the players, with Gotze apparently eager to remain with the Bundesliga champions and Lewandowski seemingly keen to leave, with his agent recently confirming transfer talks with Real Madrid.
And Scholl, who was a coach at Bayern until 2013, told ARD: "Something strange is happening.
"A player [Gotze], whose contract runs for one [more] year, wants to remain and has committed several times to the club, but this is not welcomed by the club and he allegedly must go.
"Another player [Lewandowski], whose contract runs for three years, is already talking with other clubs about a change and is still not declared for sale?
"Lewandowski does not have much cunning in Bavaria.
"He has scored 30 goals, has a three-year contract and is still negotiating with other clubs - he probably feels not too well at Bayern."