A different version of Apktool.jar from ibotpeaches
Different versions of java: in a terminal run the command update-alternatives --config java
then change the number
apt-get remove zipalign, apt-get update, go to /etc/apt/sources.list and comment out the kali repository by putting # in front of it, add this repository under it: "deb http://ftp.de.debian.org/debian buster main", apt-get update && apt-get install zipalign. Zipalign from kali repositories has a bug.
Last thing, change the apk you want to backdoor. Modern android apps are simply difficult to tamper with and have protection mechanisms.