Jean Todt has vowed to "think about" some of Red Bull's criticisms of the current rules.
"Poor Daniel did nothing wrong," he told Austrian Servus TV.
When the Australian driver was released from a pitstop with a loose wheel, he had to serve an in-race penalty but then also a ten-place drop on the grid for the subsequent Bahrain grand prix.
Marko insists: "There is a constructors' championship and a driver's championship -- as a team we should have had points deducted, or a fine.
"In my eyes it was not even an unsafe release. As Daniel drove out he said 'Hello, my wheel is loose' and so we pushed him back. There was no danger."
Another of Marko's concerns is the new and unseemly noses, after the FIA changed the rules over the winter for safety reasons.
"You can see that the nose is so low that it can go underneath the other car, lift it up and roll it over," he said.
"Unfortunately we cannot change it during the season because it is about the chassis, but we need to respond as quickly as possible for next season," Marko insisted.
"Maybe we can do something at the same time for the aesthetics of these noses," he added.
Marko said he spoke with FIA president Todt about his concerns in Bahrain.
"He took a position on various issues and promised that he would think about carrying through with the requested changes," he revealed.