Many a times it happens that your contacts get duplicated in Google Apps when you try to import contact list from another account.
It also effects when you sync your Google Apps account with your Mobile devices.
To avoid such duplication go through following steps.
Step 1: Sign-in to your Google Apps account and goto Contacts tab beside Groups on the upper side of your window.
Step 2: Then click on More where you will get a drop down.
Step 3: Select Find & Merge option from the list.
Step 4: By clicking on it it search your entire Contact book and list out duplicate contacts.
Step 5: Below there you will get a option MERGE by clicking on it all the duplicates will be removed from the contact list.