More than One Clone In Logan
There is also the possibility that there are more clones made out of Logan’s DNA. The comics had depicted X-23 as being the only surviving clone of Logan’s and that was because the lab geneticist had decided to change the sex of the subject. Logan could definitely riff off that element of the story and adapt it into the film. There could be multiple clones who are not as perfect as Laura but who have been trained to kill without warning.
Other Possible Candidates
Donald Pierce and his Reavers would be the first people to come to mind. They are the only people who hate mutants enough to want to destroy them without plausible cause. Either that or other Weapon X creations are also in store for Wolverine and his company. Anyone from Ultimaton who has an indestructible body with a capacity to destroy his opponent or Fantomex, whose DNA was infected with nano-technology making him a threatening adversary.