Naruto knocks down God Realm. He starts looking for Nagato through chakra sensing. Again, no clones created. Until this panel
http://www.mangafox.com/manga/naruto/v47/c441/15.html the first clones created. Notice how they don't disappear right after activating FRS? It's because they're getting in position. Hell, they even look like they're moving in opposite directions. Then?
http://www.mangafox.com/manga/naruto/v47/c441/17.html The smoke bomb comes
guaranteeing that God Realm will be watching the smoke cloud throughout the entirety of Naruto's plan. Meaning everything happening behind and beside him, he is unaware of do to focusing on one point. Get it? If not, keep reading.
http://www.mangafox.com/manga/naruto/v47/c441/17.html Second FRS comes out. Look at Naruto's eye. You see that? No more Sage Mode. The other two clones? Still not accounted for. I wonder what they're up to now that Sage Mode's clone limitation doesn't matter, thanks to Naruto's Sage Mode ending...
Keep in mind, God Realm is still watching the real Naruto, and the cloud of smoke that's slowly dissipating. Not paying attention to whatever's happening around him. It's that exact lack of attention that gives Naruto's clones time to blanket the battlefield with more clones, so that they all can perform henge to disguise themselves as rubble.
http://www.mangafox.com/manga/naruto/v47/c442/5.html The first two dispel their henge to try to catch him. Once they fail, all the others jump him.
http://www.mangafox.com/manga/naruto/v47/c442/6.html No sage mode, thus no clone limitation.
Here's the part where you guys get confused though:
http://www.mangafox.com/manga/naruto/v47/c442/8.html "He'd already used a Kage Bunshin." You think he's talking about dropping out clones the instant he hit the ground. Which if you read what I have above, you'd recognize as bull, because he wasn't even prepared to fight yet, nor did he admit to having any plan until the fight actually started. Sure, it's possible he would set clones just incase talking to God Realm didn't work... but remember, God Realm only knows the clones were set up before the second FRS hit him. He has no idea when they were set however. I'm sure that picture leads to confusion aswell, but since you don't see any handseals, you can't expect anyone to take a picture of Naruto sitting completely still as proof of him using Kage Bunshin. That's daft.
It's also important to remember, God Realm never saw any handseals (and neither did we). There's no reason to assume he made those clones prior to running out of Sage Mode because just like God Realm, we didn't see it happen. We DID however see him make clones for the FRS. Clones that never disappeared. Clones that were capable of making even more clones while he was busy trying to defend against the double FRS combo.
So there you go. If that didn't fix things, nothing will.