Oracle 12.1.0.2 changed some things in the data dictionary that are causing this. Specifically, the table SYS.USER$ is no longer included in the SELECT ANY DICTIONARY system privilege. So what’s happening is that Toad is detecting that you have SELECT ANY DICTIONARY, and assuming that because of that, you can select from the SYS.USER$ table.
If you can grant SYS.USER$ to the user that you are logging in as, the problem will go away. Another solution would be to upgrade to the current version of Toad.