Corrections to my comment formatting below to show the tags properly.
I found the solution to this problem in the documentation. Each “ion-menu-toggle” element should have a “menu” attribute with the correct menuId defined to know which menu to toggle open or closed.
Left-side menu changes to each “ion-menu-toggle” element
<ion-menu-toggle menu="main">
Right-side menu changes to each “ion-menu-toggle” element
<ion-menu-toggle menu="user">