Thanks for your message, but this is exactly what the command should be doing.
It's a feature, not a bug.
As clearly stated in all support documentation some commands respond to more than one shortcut and this extends their functionality. They actively listen for 'modifier' keys.
In the case of Create Magnet Target [Shift+`] creates Magnet Target while [Alt+`] creates Center Marker.
Accessing the command from the menu will only allow you to create MTs.
For more information, please, refer to Keyboard Shortcuts Map and the support section of this site.
Hope that once you look into the documentation all will make more sense.
I will now change the title of your post to a more descriptive and precise one.