Office 365 Integration on Server 2012 R2

I suggest you read this MS article:

https://docs.microsoft.com/en-us/azure/active-directory/connect/active-directory-aadconnect-topologies

Specifically this section:

Single forest, multiple sync servers to one Azure AD tenant

Having multiple Azure AD Connect sync servers connected to the same Azure AD tenant is not supported, except for a staging server. It's unsupported even if these servers are configured to synchronize with a mutually exclusive set of objects. You might have considered this topology if you can't reach all domains in the forest from a single server, or if you want to distribute load across several servers.

You CAN have one or more STAGING servers, but they are only for DR purposes and really aren't even needed short of remembering your configuration/sync settings.

If you export and document your AADConnect settings/mappings/customization then you can just as easily rebuild a new AADConnect server in a DR scenario.

You CANNOT have more than one AADConnect sync server in your environment connecting to the same Azure AD tenant.

This issues may caused by that you have not add your domain to office 365.

First , we know that Office 365 uses the cloud-based user authentication service Azure Active Directory to manage users. Every Azure AD directory comes with an initial domain name in the form of domainname.onmicrosoft.com. The initial domain name cannot be changed or deleted, but you can add your corporate domain name to Azure AD as well.

For example, your organization probably has other domain names used to do business and users who sign in using your corporate domain name. Adding custom domain names to Azure AD allows you to assign user names in the directory that are familiar to your users, such as ‘alice@contoso.com.’ instead of 'alice@.onmicrosoft.com'. The process is simple:

1. Add the custom domain name to your directory
2. Add a DNS entry for the domain name at the domain name registrar
3. Verify the custom domain name in Azure AD

You can add your domain in Office 365 portal just here:

If you plan to federate your on-premises Windows Server AD with Azure AD, then you need to select the I plan to configure this domain for single sign-on with my local Active Directory checkbox when you run the Azure AD Connect tool to synchronize your directories. You also need to register the same domain name you select for federating with your on-premises directory in the Azure AD Domain step in the wizard. You can see what that step in the wizard looks like in these instructions. If you do not have the Azure AD Connect tool, you can download it here.

More about how to add a domain and users to Office 365, refer to this official document.