So karkat doesn't believe in the ancestors even though he made them. How does that make them not clones? Wouldn't he know about them regardless of whether they were clones or not? I thought that the main trolls were paradox clones of themselves and the beforus trolls were somehow love or hate babies of the others (devided by prospit/derse)

See, the way Ectobiology works is that you have to track down the clones, copy them, and then they mix and create the other set of babies. John had it easy because Mom had already locked the targets, but Karkat would have to track his group down through the screens, get the Ectoslime and create themselves. However, Karkat doesn’t believe in the Ancestors- Which means he cannot have cloned them, because otherwise he would’ve SEEN them on the screens, in the past of Alternia, their adventures and lives! Given he thinks it’s just a ‘random set of extra wigglers’, it’s only possible for Karkat’s Group to be a bunch of clones of themselves, and Meenah’s Group to be their genetic offspring.