Ubuntu not booting after cloning (OSX and Kali)
OK, after searching for 2 days I finally got the answer.

So I had a bootable apfs OSX partition with rEFInd installed from OSX. rEFIND couldn't find ext4 partition from OSX natively. That was the problem. ext4 partition was cloned from source later on.


Download Kali live-USB, mount it using dd or rufus or any other software. 
Reboot, Hold alt to boot from Kali USB, then follow the instructons from here https://medium.freecodecamp.org/kali-installation-on-usb-stick-with-pure-efi-boot-on-a-mac-37585b7698e2 section "Boot from Live GRUB".
After you log in (here's the main trick): download a debian version of rEFInd (.deb)
and install it:


sudo dpkg -i DEB_PACKAGE


Reboot. Your Kali partition should appear on rEFInd boot menu together with OSX.