I think this is just because "SHAREPOINT\system" is actually a "logical" account that has no real "physical" correspondence, while "domain\user" is something that maps to an actual user, in this case a AD domain one. For these reason, I would assume SharePoint filters out the SharePoint\System user from the group members section in the web UI while it retains it when using PowerShell - which usually is used by more "advanced" users.
As a side note, "SharePoint\System" is just a name that SharePoint uses when an account is given system-level permission. Most of the time, this means that you are either using the Farm account or the account the current app pool is running as (this can actually be modified in the Central Admin - there should be an "Act as system" privilege, active by default, that you can toggle in the User Policies section for a web-application).
Anyway, what you are experiencing it completely normal AFAIK, so you probably shouldn't give it much importance.