P: The Cmd key selection is totally messed up.

Different issue.

Please reference the new conversation here: Photoshop: Action error Select Command not found

Photoshop CC 2015.1.2 Windows 64-bit won't run Actions which call for the "select" command {not found}. This is a real bummer. BUG BUG BUG BUG. Adobe is turning Photoshop into Apple's Quicktime issues.

OS - Windows 10. Tried resetting perf. and settings, restarting PC and opening PS without tablet attached.

NOT SOLVED!
Bad Photoshop cc, please fix this.

Its too frustrating, updating Photoshop to latest update release 2015.1.2 but still Auto-select behave strange. I have found the culprit "DAMN SHIFT KEY COMBOS".
My fix is as follows, where ever you come across selecting multiple layers while pressing "Ctrl" key press-N-hold "Shift" key to isolate the layer being selected unnecessary. Photoshop takes "Shift" key as pressed on it own. Wohh!!

Wacom tablet behave strange in man ways in this release of Photoshop. Painting and editing workflows is ruined now.

I had the same problem (with mouse, not wacom) and it is now (hopefully completely!) gone with the 2015.1.1.
But I am working always on new files at the moment. Maybe you try fresh documents, reset all your settings (but store them) and try to reset maybe even PR-Ram of the computer. Check also the settings of the move tool, which are influencing the Cmd-Key.
Or maybe try to work from another fresh user account with fresh preferences. These are the only ideas I have to pinpoint the problem.

I am Command+Selecting the layer from the Layers Panel. I do have a wacom tablet plugged in, though it still happens if I select the layer via the tablet or trackpad on my computer.

Are you selecting on the canvas using the move tool or by clicking on Layers in the Layers panel?

It's same for me! The issue appear when i'm using Wacom table!

yeah, same issue STILL (1/13/2016)
on MBPro Retina 2015
running el capitan 10.11.2

just updated to latest version of PS CC and the multiple layers selected will unselect as I Command+Select additional ones. It feels very random. Things will work for a while, and then suddenly the application doesn't know I'm holding down the Command key at all, so I'll have to keep trying to reselect my layers until it finally 'sticks'. It's hard to replicate consistently, but it will happen without fail during the course of my working in a file.

I just wanted to go back to select more than one layer using cmd or any other shortcut. In the new version is impossible, what happened? Why did it happen workflow change?