Different "free space" indications in Macintosh HD after upgrading to El Capitan
I have a solution! You need a clean up spotlight index.
Go to Preference - Spotlight - confidentiality. Press "+" and 
add whole disk to this. Check it in confidentiality list. After this - remove (by press -)

Turn off you mac. And boot with "safe mode" (by pressing shift + power button, until apple logo will be on display). Please be patient, safe mode loading not fast. And you may have some 'monitor artifacts'.

Check you disk space now. All good? If yes - just reboot again in normal mode.

p.s. this is solution, I got from Apple Care by phone.