Yes, the issue is with the size of the logo. The logo image itself has a lot of white space around it it would be best to trim the white space from the original logo and upload a new image for the mobile header.
Alternatives are:
1. Reduce the Mobile Menu Item height in Customizer > Layout > Primary Navigation.
The logos display size is based on that value.
2. If you don’t want to reduce the menu item height – add this CSS:
.mobile-header-navigation .site-logo.mobile-header-logo img {
height: 60px;
}