This is where things get tricky. After completing a few "go here, do this" missions after beating the Elite Four, you're given the ability to find Mega Stones at night. Between 8PM and 9PM (real time), you're sent off to find locations around the world where the ground is sparkling. If you interact with these spots, you'll get a Mega Stone. The rest of the day? They're simply not there.
Update:Don't understand the part “go here do this“?
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Basically if you want the megastones for certain pokemon, you have to wait till 8pm to find them, you can only get megastones between 8pm-9pm. After that you have to wait till the next night to attempt to find more of them. If it's not the right time you can't see the stones and therefor can not get them.
The stones have set locations that you can find a list of on forums. And if this still doesn't explain it well enough look up megastone locations on youtube and you'll see how to find them.
I have played pokemon Y since release and have yet to even know what "Go here Do this" part is that you're even speaking of. And Ive done the side missions.
Yeah the spots are only there during those hours so you need to find as many in the hours time. They only appear during those hours so don't ask me why but only 8-9 PM are your Mega Stone Hours. The Go here do that is something that Professor Sycamore will tell you about at some point.