If you want to make clones of the PCs in your game, remember that all you need is a tiny DNA sample, which is trivially easy to get from almost anywhere they've been. A flake of skin, a loose hair. They'll do fine if your cloning technology is any good at all. (If magic exists, you can also do this with magical doppelgängers.)
What can you do with clones of PCs? What can't you do?!
Have the heroes harassed or arrested for crimes they didn't commit. Witnesses positively identify them as the culprits. Surveillance video shows them doing the deeds. Begin as a mystery that they need to get to the bottom of.
Or be up front and have the clones meet them face to face. Maybe the clones have escaped and want help. Maybe the clones are trying some convoluted confidence scheme. Maybe the clones want to kill the originals and take over their lives. Maybe the heroes catch a glimpse of the clones in the distance, recognise them as copies, but are unable to intercept them. Now they know they're out there...
This assumes fully grown age-accelerated clones. What if the clones are babies, or children? The heroes might save them from whatever evil scheme the villain has... but then what do they do with them? The rescued kids are literally their own flesh and blood. And maybe society isn't ready to deal with villain-produced superscience clones, so it's up to the heroes to figure it out.
Chewbacca: You're saying this Vader clone is Nute Gunray?
R2-D2: No no, Nute's not here at all. He's masterminding the whole thing remotely.
Luke: Is it the bear comedian back on Kamino?
Miss Piggy: Fozzie? No, he's a clone of Chewbacca.
Chewbacca: What? How would Nute have got a DNA sample from me?
Miss Piggy: When you were imprisoned on Bespin.
Chewbacca: This is getting, dare I say it, even weirder.
R2-D2: No, Nute's far too clever to show his face in this adventure.
C-3PO: He doesn't even have a face any more.
R2-D2: Yes! And he's using that to his advantage.