It sounds like it's displaying phone numbers in the format for another country.
The easiest way to force this is by using prefixes; for example, if I type +11234567890, I get "+1 (123) 456-7890", but if I type +811234567890 (Japan prefix), I get "+81 12 3456 7890", the correct format for Japan (which looks like what you might be getting).
Places you can adjust default behavior that might be relevant:
Under Contacts Preferences, General tab, make sure that you have the correct country selected for Address Format. You can also set this on a per-card basis, although I'm not sure whether it affects phone number formatting.
Go to System Preferences, Language & Region pane, and make sure your preferred language is correct, that you don't have any undesired languages in the list, and that the region setting matches your region. I've occasionally seen Macs at work default to Afghanistan instead of the US for some reason, which causes some odd display issues like that.
While you're in there, confirm that there aren't custom settings for any apps in the other tab.