The on/off (visible or not) status for Layers on the Map does NOT correlate -- by DEFAULT -- to the on/off (visible or not) status of the Legend Items in the Layout.
In other words, ALL Legend Items in the Layout Contents are tuned ON by default (see below); regardless of whether they are turned ON or not in the Map Contents (whether you like it or not;).
This doesn't seem intuitive and can be confusing -- at least, initially.
So, my recommendation is to the have these correlated by default.
Then, the User can make changes, if necessary, from that starting point.
![Map Layer visibility vs Layout Legend checkmarks.png Map Layer visibility vs Layout Legend checkmarks.png](https://community.esri.com/t5/image/serverpage/image-id/62669i816438BA5D87B405/image-size/large?v=v2&px=999)