This is expected. MainStage does not offer control surface support, and will treat incoming data from control surfaces as normal MIDI data. This may lead to unwanted triggering of notes, or other undesired results. Avoid using control surfaces when running MainStage.
MainStage: Pressing buttons on a control surface triggers notes
When you press buttons or controls on an attached control surface, notes are triggered on the currently selected instrument in MainStage.
Information about products not manufactured by Apple, or independent websites not controlled or tested by Apple, is provided without recommendation or endorsement. Apple assumes no responsibility with regard to the selection, performance, or use of third-party websites or products. Apple makes no representations regarding third-party website accuracy or reliability. Risks are inherent in the use of the Internet. Contact the vendor for additional information. Other company and product names may be trademarks of their respective owners.