PD11 is shared between the camera connector ISI_D6, Audio CODEC IRQ, an Arduino connector, and Xplained Pro extension header 2 GPIO (EXT2). PD11 is pulled low strongly by the Audio CODEC and the pin is not usable by any other source unless it is disconnected. Removing R200 will disconnect PD11 from the Audio CODEC interrupt pin freeing it up to be used for camera and extension applications.
PD28 is shared between the camera connector ISI_D9, Arduino connectors, LCD extension connector IRQ1 (EXT4), and Xplained Pro extension header 1 IRQ (EXT1). If a camera with 10-bit mode is used together with a display connected to EXT4 the display IRQ line will conflict with the camera.
On revision 6 of SAM V71 Xplained Ultra pin 41 (DISPLAY ENABLE) on the LCD connector is not connected to anything (floating).