Sometimes there's quirks with the standard metadata types - it's expecting it to be in your source as every org has two AppMenu files (
Salesforce1.appMenu). Since it's not there, it seems it attempts to delete it (which isn't possible).
You'll either want to do one of the following
- Retrieve the
AppMenu metadata from your source org into your repository
AppMenu in your
.forceignore file for source commands so it ignores this metadata type in CLI source commands.
I'd recommend ignoring it as it doesn't add any value in your source - there's issues deploying it as such to re-order app menu items and users can easily customize the order of apps that display in the app launcher in Lightning anyway.
You can see an example of this being done in the lwc-recipes repository for certain standard metadata which includes appMenus
# Standard metadata
# LWC configuration files
# LWC Jest