Probably, because he didn't get access to their DNA, that's the most reasonable option.

Indeed, Yahiko's Pain body was in the mausoleum that Konan put it in, and only Obito had access to it. Konan was presumably thrown into the lake that surrounds Amegakure and thus like Jiraiya was completely inaccessible.

The real question however is both how did Kabuto acquire Nagato's DNA...and how did he know that Nagato was the real Pain? Per chapter 489, he already had Nagato ready to go, only one arc after he died in Konoha. No blood was shed there and Konan took possession of his body before anyone else had access to him. Even Obito didn't know where his body was at that point. Which means that Kabuto or Orochimaru knew that Nagato was the real Pain, long before it was something revealed in the main story. Either Orochimaru figured it out or Kabuto got the information as a spy. It could be that Danzo told Orochimaru when he was working with ROOT, and Orochimaru retrieved Nagato's blood or hair from the battlefield where Hanzo betrayed him.

he got madara's dna........how difficult it would be to get their dna(konan and yahiko).

Plot magic says that Black Zetsu was ultimately responsible for Kabuto acquiring Madara's DNA, without Kabuto even being aware of it. We don't know how that works. But somehow, he managed to fool everyone from Hagoromo, Hamura and Indra down to Madara, Kabuto and Obito. Black Zetsu seems to be even more adept at Jedi Mind Trick that Darth Jar Jar (if you believe in that theory) :D

I also wonder how BZ managed to show Kabuto Maadara's corpse (yeah, BZ said he led him exactly to the corpse itself) without Kabuto and Obito even noticing it. Ok, Kabuto could've attribited it to the pure luck, but I mean, Madara's grave wasn't hid in some random place, was it? It's pretty strange for Obito not to watch out for this corpse, he must've known where it's buried. And if it had been gone and Obito already knew about it, he didn't have to be so shocked after seeing Madara in Kabuto's reanimations collection.

Jedi Mind Trick :D There is literally no other way

1.) Kabuto could not find either corpses 2.) because they betrayed the Akatsuki 3.) Konans body was lost at sea could not be found 4.) yahiko could not be used withoug chakara rods and kabuto didn't have the power to do that 5. He could not take over yahikos body with out rinnegan and yahiko had an imitation rinnegan 6.) Obito might have destroyed their bodys and or told kabuto not to use them.

yeah and suddenly he found nagato's dna eventhough he was warned not to approach him or other ame orphans by obito...............that's pretty lame excuse.and konan 's body was floating remember.

Edid to the 4 and 5: black receivers play no role for the reanimation jutsu. All that Kabuto needs is just a sample of DNA, not necessarily the whole corpse. If Kabuto had got Yahiko's DNA, he would've easily reanimated him regardless. It's the Edo Tensei Kabuto uses, dude, not the Six Paths of Pain jutsu, so the person is reanimated within a body of the sacrifice and not it's own one, that's why the reanimation and it's dead corpse can effectively co-exist (as seen when Edo-Sasori fought against Kankuro using his own puppet body). Edo Tensei does require neither Rinnegan nor receivers to revive and control someone.