There must be misconfiguration and allows the score rate higher. Observe closely, how the legit email marked as SPAM in the filter.
Yeah i don't want to bypass our spam filter as 93% of all emails to our domain is spam. The spam filter is doing its job 100%, it's something at O365 that's causing the issue, whether it's some settings i have/haven't set. The spam filter does generate a quarantine report but 99.99% of it is spam. Hello, The emails pass through the spam filter (otherwise they wouldn't appear in the Junk Folder) its when the emails reach O365 they are getting put straight into the junk email. However, that will mean getting a lot of spam :-( You can always bypass the spam filter by simply changing your MX record. Additionally, does your spam filter generate a quarantine report letting the users know what was blocked? Once you know the reason, you can take preventive measures so good messages won't go into spam.
The third-party spam filter you're using should tell you the reason why messages are being blocked.