Sitting for 24 hrs might have left the dye dry, but when you applied the conditioner, you effectively re-wet it, because the conditioner will soak into the pores of the leather. If there's any dye particles that haven't attached themselves.....they're free to leave on whatever they can rub against, whether that's your pants, your shirt, or your thread. I've gotten far better results since I started airbrushing the dye, but even with that method of application, I still get additional rub off after conditioning.....not a lot, but it's there. And USMC Black has a reputation for significant rub off.
Dye, dry, buff, buff, buff,......... condition, buff, buff, buff, buff, dry, buff again to see if you've still got any loose dye particles, and if not, then stitch.
Yes, once the conditioning has completely been absorbed, you can seal the leather and it'll help prevent rub off.....but only if you've got 99+% of the dye particles buffed off. The sealer is to protect the leather, not to glue down loose dye particles.