O365 internal emails going to junk folder.

We are on O365 and have noticed that internal emails sent using this method, mostly option 2 (https://docs.microsoft.com/en-us/exchange/mail-flow-best-practices/how-to-set-up-a-multifunction-device-or-application-to-send-email-using-office-3), are sent to the junk mail folder. On most occasions we right click and tell it to trust our domain. However on a certain email they keep going to the junk mail folder even though we tell it to trust the domain. I am going to double check with the person who handles the script/application that sends the email to see how they are doing it because the strange thing i see is that it says its coming from, device@domain.com, but when i do a message trace on the O365 admin side it shows the person who initiated the script/application.

The way the script application works it we are using sharepoint and our sharpoint admin created a page/site that allows a user to request a check. They fill out a form and then when they hit submit it goes to the person they request the check from.

So if Bob Smith is the one doing the check request it's sent to the person he choose from the drop down and when that person sees the email it looks like it's coming from device@domain.com.but the message trace shows the person who initiated the check request.  

I don't know where on the O365 admin side i look at for internal rules. I'm thinking since its uses the smtp relay it seeing it as an outside email? But I am not sure.