Before finally settling on him being the son of Professor Paradox, he was going to be either the son of Eon, Ben 10,000, or Paradox. Ironically, if either of the other two choices had been finalized, it still would have made sense why Xarlek has a grudge against Ben.
Eon: Eon wants to be the only Ben Tennyson, and would want revenge for the two times Ben has defeated him in the past, thus making him encourage Xarlek to carry on his work.
Ben 10,000: Ben 10,000 is a busy person, and is occasionally unable to be home with his family. Due to him not being around Xarlek a lot, Xarlek would begin to hate him for being a poor father figure, thus making him want to defeat his father's younger self, so he could be born as another person's son.