Defender keeps scanning reported and ignored files

So we have Defender installed on multiple sites and configured for weekly scans. But the results of these are pretty inaccurate. It will routinely detect the same issue multiple times. we're getting literally hundreds or thousands of completely irrelevant security warnings on almost every site.

Please see images:
https://static.livechatinc.com/8801096/OU126C2EF7/41c00eed5ead7f237ad8559f7679684d/Screenshot%20(1).png
https://static.livechatinc.com/8801096/OU126C2EF7/ea7587f03ede99db2a9662782d7d8b23/Screen%20Shot%202017-08-02%20at%2016.01.53.png