It looks like something in KB4012216 and KB4012204 breaks the CRM associated views. For example if you load up an organisation record and click on contacts or any other associated view the blue bar loads half way up the page and the records don't load as shown:

I just uninstalled both of these KBs and it fixed it.
Why both? Surely only one of these is the problem! I hear you ask.

Here is an excerpt from KB4012204

The fixes included in this Security Update for Internet Explorer 4012204 are also included in March 2017 Security Monthly Quality Rollup. Installing either the Security Update for Internet Explorer or the Security Monthly Quality Rollup installs the fixes that are resolved with this update.

So if you have either of those updates installed, then you need to remove both of them to fix this issue. Or be a better admin than me and find out what setting you need to change in IE to actually fix this issue rather than delay it.

This issue affects Internet Explorer and as a result, the CRM Client for Outlook.

Update2:

KB4016635 has been released for Windows 10 that fixes this issue.

KB4016446 has been released for Windows 7 that fixes this issue.

As stated in the KB articles, to get these updates you need to go to http://www.catalog.update.microsoft.com and search for them. You can also manually import the updates into WSUS

Big thanks to reddit user u\Either_Orlok for letting me know about the new windows update that fixes this issue.

Update1:

From the Dynamics Community

It seems that there is a problem with the CSS on the server. To fix it, you can either wait until a hotfix has been released from Microsoft, or you can do the following workaround.

Go to your CRM server and make a backup of "%ProgramFiles%\Microsoft Dynamics CRM\CRMWeb\_common\styles\global.css.aspx" and then edit the original file.
You will need to add the following to the bottom of that file:

table.ms-crm-Form-Layout span[type="subgrid"] {position:static !important}
td.AdvFind_td_FindBody {display: table-caption;}
textarea.ms-crm-Input {height: 100px !important;}

Instruct your users to press Ctrl + F5 to reload the CSS in their browser.

There are still quite a few things wrong with the views on the CRM it seems but this will fix the issue for the Associated Views, Advanced Find and Notes.