Q: Magic mouse not scrolling after sleep

But you haven't given us the key info.   Is it an older Magic Mouse 1 or the new Magic Mouse 2?    Now that you have upgraded, the MM1 will only partially work with El Capitan.   You will need to buy the new Magic Mouse (MM2) to be assured of full functionality with El Cap and its successors.

An apple article is there : If your Apple wireless mouse, keyboard, or trackpad aren't working as expected - Apple Support

I hadn't heard that - could you post a link to the info that the original MM cannot be used in EC and beyond? As far as I know, older mice may not include all the new features, but the basics should work with whatever OS is running.

It sounds as though bluetooth may not be connecting the two devices properly; resetting the SMC will sometimes help (follow the instructions for Notebooks):

https://support.apple.com/en-us/ht201295

And, you can also try to re-pair the mouse with the computer (in Bluetooth Pane).

Yes, that is why I said the MMI will only work partially with El Cap.    It will work to some degree, but most of the complainants here do seem to suggest their problems were resolved with MM2.   It is unlikely Apple would specify exactly, they want to sell the new version.

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This is what I saw (which doesn't mention much in differences except the built in battery):

http://www.macworld.com/article/2994798/input-devices/apple-magic-mouse-2-review -mouse-unable-to-conjure-up-any-innovation.html

I know they want to sell the new one; however, everyone with a notebook older than this year's model, wouldn't be able to use their trackpad either. There again, the basic functions such as the subject of this thread, should work no matter the age of the device. That includes waking up, scrolling, being able to unhide dock/menu bar, etc, etc. That should have absolutely no effect - the new one simply has the capabilities that are being introduced in the new OS. If you don't use them, no need to spend more money. And, not having the new features should not have anything to do with the basic functions of a mouse or trackpad. I've had all the newer features turned off in the trackpad/mouse Pref Pane because of my semi-limited use of fingers and my very, very old one button mouse works just great with my new iMac as well as El Capitan.

I have this same problem.  The link below is useless.  Please help.  Also if I go to System Preferences and to the Mouse,  and t go to "Set Up Bluetooth Mouse" it does not see it.  Thank you

Which link is useless?

Have you tried to reset the SMC?

Have you tried to re-pair the mouse? Turn it off and then on and see if it'll pair.

By restarting the computer, you are - essentially - doing a reset. That means there is a communications error. I cannot tell if that would be a software or hardware problem; there were some major changes made in El Capitan which resulted in similar behavior on my iMac with several external hard drives. I would suggest that you take advantage of your warranty and either contact Apple support and/or make an appointment at your nearest Genius Bar. (In my case, it was the changes made to the OS which did not communicate with the external drives).

Thank you.  I was referring to the first answer to the original post, as I had not seen the entire thread.  But your suggestion of resetting the SMC seems to have worked for me.  So far so good.  Thanks again!

Great to hear it!