Issues after waking up from sleep, macbook pro

Question

Macbook Pro, retina display, mid 2014, 2.6 GHz i5
Yosemite 10.10.1
This problem started about 4 days ago. If I let my computer sleep for a over about an hour, one start up I have lots of issues. It is hard to explain what it is, so I'll explain what I am capable of still doing. The cursor works as in I can move it, but I cannot click anything. Also there is no "hover over" capabilities, like if I hover over something on the dock it usually won't say the programs name. The windows I had open are still there, but I cannot minimize or close them (as I cannot click).
This started like 4 days ago, I have tried a few fixes. One of which was upgrading to Yosemite, I was running Mavericks when it started. The problems persists. I then talked to someone from apple who suggested a SMC reset, but the issue is still there.
The only way I have been able to "fix it" is if after a start up the problem is there, close the lid for a minute, then open it back up. The issue usually then solves itself.
Any help would be greatly appreciated.

Answer 1

When you have the problem, note the exact time: hour, minute, second.  
These instructions must be carried out as an administrator. If you have only one user account, you are the administrator.
Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad and start typing the name.
The title of the Console window should be All Messages. If it isn't, select
          SYSTEM LOG QUERIES ▹ All Messages
from the log list on the left. If you don't see that list, select
          View ▹ Show Log List
from the menu bar at the top of the screen.
Each message in the log begins with the date and time when it was entered. Scroll back to the time you noted above.
Select the messages entered from then until the end of the episode, or until they start to repeat, whichever comes first.
Copy the messages to the Clipboard by pressing the key combination command-C. Paste into a reply to this message by pressing command-V.
The log contains a vast amount of information, almost all of it useless for solving any particular problem. When posting a log extract, be selective. A few dozen lines are almost always more than enough.
Please don't indiscriminately dump thousands of lines from the log into this discussion.
Please don't post screenshots of log messages—post the text.
Some private information, such as your name, may appear in the log. Anonymize before posting.