As IGN puts it "if the door on the far side of the lava pit in Sector 3 after you leave the desert refinery via the elevator is red, you're stuck." The offending door can be seen in the image above. Nintendo is aware of the issue but there is currently no solution to this problem.
According to YouTube users kNIGHTWING01, the glitch is caused by saving the game after beating the area boss for the third time. Apparently, if players save the game after beating this boss but before opening the door in question, it will remain locked and cannot be opened. Should this occur, the only way to fix the glitch is to load an older save file or start the game over from the beginning (unskippable cutscenes and all). See a video of the glitch below.