Collection Error, Tables missing clustered indexes, Tables missing primary keys (4337704)

Alarms:

"Tables missing clustered indexes" "Tables missing primary keys"

First, make sure your SQL Analysis is turned off since this is sometimes one of the causes of that alarm due to a lot of overhead. 

If they all failed to return data within allowed 5 minutine these alarms can also trigger. It is not a defect but a part of the Diagnostic Server design: if it takes more than 5 minutes for queries to get results from monitored server, the Diagnotics Server deliberately fails them.

IN regards to the database's tables are missing clustered indexes and primary keys.
You can look in the Reporting and Trending section.
To get this information to display you will first need to select the Report tab on the ribbon. Then complete the Repository, select the connect/s and select the time range.
Then go to Reporting and Trending > Views > SQL Server Health > Tables Missing Clustered Indexes or Primary Keys.
There are 2 grids which will give you the Server, Database, Table, Owner and Schema details.
The grids do not refresh automatically. You may need to refresh manually.
Once you have this information you can go to the connection's Databases drilldown and look for some of the answers there. In the Databases grid select the particular database and then select the Indexes tab below. Select an index and then the Fragmentation tab. Expand each IN_ROW_DATA. The details here will help you. If fragmentaion is high then you should address it.

If you want to disable this alarm, - from Configure tab, click Scheduling icon, scroll it down and you can disable the scheduling of the 2 collections that are triggering this alarm on this specific server only.  This way the other collections on this server will not be affected, and neither will any of the other servers.

You will need to go to Scheduling.  In the drop down box "Select connection to configure" at the top of the dialog select the specific connection that you want.  Then Scroll down the list of collections to the end of the list.  Near the end of the list are the 2 collections you are looking for - "Table Missing Clustered Indexes" and "Table Missing Primary Keys".  By default they are not collected in the background and only collected at 12:00 Am every day for reporting purposes.  This is what has been failing mostlikely due to not delivering this info within specified time.  If you select the first of the two collections and then select the "Override" checkbox below, you can unselect the "Store reporting" checkbox.  Repeat for the second collection and then restart the Quest Diagnostic service.