Installing virtualbox guestadditions fails with the error message that the kernel headers cannot be found.

This has been reported in this bug already: https://bugs.kali.org/view.php?id=2044

I create a new issue because I'm not sure that 2044 corrects the origin of the problem.

The VB installation script determines the header directory like this:
:
KERN_VER=uname -r
KERN_DIR="/lib/modules/$KERN_VER/build"
:

Test:

root@MEDUSA:/> uname -r
4.3.0-kali1-amd64

Check the place used as base directory by the script: /lib/modules

root@MEDUSA:/lib/modules> ls
4.3.0-kali1-amd64 4.4.0-kali1-amd64

root@MEDUSA:/lib/modules/4.3.0-kali1-amd64> ls
kernel modules.builtin modules.dep.bin modules.softdep
modules.alias modules.builtin.bin modules.devname modules.symbols
modules.alias.bin modules.dep modules.order modules.symbols.bin

root@MEDUSA:/lib/modules/4.4.0-kali1-amd64> ls
build modules.builtin modules.devname modules.symbols.bin
kernel modules.builtin.bin modules.order source
modules.alias modules.dep modules.softdep
modules.alias.bin modules.dep.bin modules.symbols

The build scripts are actually located in 4.4 whereas uname points to 4.3.

This mismatch in uname/directory might indicate a packaging bug.

Best regards.