Only way I know of with gnome3 is to remove and install it again. I use cinnamon DT and it provides a way to edit the icon command ( should be VirtualBox %U ). You can always ask the Fedora folks or maybe someone here that uses gnome will pop by.
What is the purpose of the virtualbox.desktop file and here are the contents:
cat /usr/share/applications/virtualbox.desktop
[Desktop Entry]
Encoding=UTF-8
Version=1.0
Name=Oracle VM VirtualBox
GenericName=Virtual Machine
GenericName[de]=Virtuelle Maschine
Type=Application
Exec=VirtualBox %U
TryExec=VirtualBox
Keywords=virtualization;
Keywords[de]=Virtualisierung;
MimeType=application/x-virtualbox-vbox;application/x-virtualbox-vbox-extpack;application/x-virtualbox-ovf;application/x-virtualbox-ova;
DocPath=file:///usr/share/doc/VirtualBox-5.1/UserManual.pdf
Icon=virtualbox
Categories=Emulator;System;
Comment=Run several virtual systems on a single host computer
Comment[de]=Mehrere virtuelle Maschinen auf einem einzigen Rechner ausführen
Comment[it]=Esegui più macchine virtuali su un singolo computer
Comment[pl]=Uruchamianie wielu systemów wirtualnych na jednym komputerze gospodarza
Comment[sv]=Kör flera virtuella system på en enda värddator
Comment[ko]=가상 머신
That is exactly what mine shows. However as I said other than the original install I don't use gnome, hate it and install cinnamon as soon as I get the install settled down. I would really do the install again because something must be missing.
Hm but we use DNF and the reinstall option doesn't take. Since we have a huge Windows 7 VDI I didn't want to risk losing association with it by uninstalling and then fixing the permissions with /sbin/rcvboxdrv setup
dnf install gcc kernel-devel VirtualBox
Last metadata expiration check: 1:06:55 ago on Wed Sep 21 15:41:06 2016.
Package gcc-6.1.1-3.fc24.x86_64 is already installed, skipping.
Package kernel-devel-4.6.7-300.fc24.x86_64 is already installed, skipping.
Package kernel-devel-4.7.2-201.fc24.x86_64 is already installed, skipping.
Package kernel-devel-4.7.3-200.fc24.x86_64 is already installed, skipping.
Dependencies resolved.
===============================================================================================================================================================================================
Package Arch Version Repository Size
===============================================================================================================================================================================================
Installing:
VirtualBox x86_64 5.1.6-1.fc24 rpmfusion-free-updates 25 M
VirtualBox-kmodsrc x86_64 5.1.6-1.fc24 rpmfusion-free-updates 780 k
akmod-VirtualBox x86_64 5.1.6-1.fc24 rpmfusion-free-updates 27 k
akmods noarch 0.5.4-3.fc24 rpmfusion-free-updates 25 k
gsoap x86_64 2.8.28-2.fc24 fedora 266 k
kmodtool noarch 1-23.fc24 rpmfusion-free 17 k
Transaction Summary
===============================================================================================================================================================================================
Install 6 Packages
Total download size: 27 M
Installed size: 96 M
Is this ok [y/N]: y
Downloading Packages:
(1/6): akmod-VirtualBox-5.1.6-1.fc24.x86_64.rpm 1.2 MB/s | 27 kB 00:00
(2/6): kmodtool-1-23.fc24.noarch.rpm 1.8 MB/s | 17 kB 00:00
(3/6): VirtualBox-kmodsrc-5.1.6-1.fc24.x86_64.rpm 3.3 MB/s | 780 kB 00:00
(4/6): gsoap-2.8.28-2.fc24.x86_64.rpm 994 kB/s | 266 kB 00:00
(5/6): akmods-0.5.4-3.fc24.noarch.rpm 2.0 MB/s | 25 kB 00:00
(6/6): VirtualBox-5.1.6-1.fc24.x86_64.rpm 6.5 MB/s | 25 MB 00:03
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 5.3 MB/s | 27 MB 00:04
Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction check error:
file /usr/bin/VBox from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/bin/VBoxTunctl from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/bin/vbox-img from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/applications/virtualbox.desktop from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/128x128/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/16x16/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/20x20/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/32x32/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/40x40/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/48x48/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/icons/hicolor/64x64/apps/virtualbox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
file /usr/share/pixmaps/VBox.png from install of VirtualBox-5.1.6-1.fc24.x86_64 conflicts with file from package VirtualBox-5.1-5.1.6_110634_fedora24-1.x86_64
Those are rmpfision builds and you would need to ask them. If that is what you installed in the first place that could answer why you are having issues. We only support the official version from virtualbox.org.