Its either a plot-hole or something is freaking messed up.

[Moe22]

It's similar to Naruto's wind release. He didn't know he had it until training or something...

 

[DeadManWonderLand]

He didn't even know about the mangekyo at that point.
He passes out how was he suppose to know he had new powers ?
It wasn't until the sasuke retrieval arc and the training thereafter that he had unlocked a power similar to what sasuke was searching for.

 

[gshine]

im a newbie but didnt obito unlock the ms n since the eye kakashi has is also obitos was also unlocked

 

[NoMoreLove]

Im so surprised no one ever once mentioned Kakashi's stamina.. He probably knew about his MS but obviously couldn't use it. He could barely compose himself after extended sharingan use much less Mangekyou Sharingan. Im gonna say that he did intensive training to allow his body to use MS during the time skip. Also I could be wrong about this but what child have we seen that had enough stamina to use a MS? None (as far as I know) Sasuke is an exception due to his Uchiha bloodline. Now that's another point. Kakashi isn't an Uchiha so its harder for him to use the sharingan in general due to lack of Chakra reserves. Theres your answer #noplothole

 

[Sherlock.]

I was going to say the strain thing.... but since you don't want to hear it.... Probably PNJ....