it's his first day using this power,he's not accustomed yet to this power,what's more kishi is trying to downgrade naruto's power each time by forbidding the use of clones,at first it was in SM he couldn't fuse with frogs,then he couldn't make more than two clones,then in KM he says he can't use clones then he makes naruto use a lot of them(the ones that ran to different battlefields),then afterwards against obito when he reverted back to KM after using BM,why he didn't make more than one clone?
the answer is obviously plot because he could have overwhelmed obito alone,so he has to dongrade him again,so that obito holds his ground until madara arrives