Throughout the Ben 10 franchise, various changes in the continuity, otherwise known as retcons, have been made. Below are most of the retcons made in the franchise. According to Matt Wayne, they take what they want and ignore what they don't like.
Ben 10: Alien Force
The Plumbers are now an intergalactic police force, when it was established in the original series that they were a secret government organisation comprised of humans only, and several with a racist attitude towards aliens.
Gwen's powers are now alien in origin, inherited from her grandmother Verdona, as well as magical.
Kevin's backstory, species, and his power's origin have been altered for the series.
He is now an Alien hybrid with the ability to absorb a shell of material around his body instead of a mutant that has the ability of absorbing, storing, and redirecting energy.
His father Devlin Levin is a Plumber that he received his powers from and was partners with Max instead of a mutation that no-one knew where it originated from and it is responsible for his parents to kick him out.
The Forever Knights now have different factions instead of being one whole group.
Ben 10: Ultimate Alien
It is revealed that Kevin's stepfather is actually a good person and that Kevin wasn't kicked out, but he went insane with power, destroyed the house, and ran away.
The queen in Ben 10: Alien Swarm has been changed into a decoy queen created by the real queen to avert suspicion towards her.