I have the same problem and I'm having a devil of a time editing the contacts (other than manually). I had this same thing happen on my iPhone and had to resort to paying for a 99 cent app for killing duplicate contacts. I had over 99 of the same contacts in multiple places.
This is highly annoying and it's frustrating that there isn't an easy solution.
Since installing the official Facebook app update, it's added another facebook account sync option, which has all the duplicates in it. Unticked that in the contacts display options and they've all dissapeared.
Wonder why the newest Facebook update has added that?
Funny you should mention that - since downloading the Facebook app update, it slows the whole OS down to a crawl until I kill the Facebook process.
If does seem to be incredibly badly coded. The mobile web interface is much better.
I've done the contacts/menu/display options, and also gone to display only those with phone numbers. I still have many duplicated entries. I'm thinking my old phone synced all my Facebook, T-Mobile, and Gmail contacts together into my Gmail account as well as my T-Mobile account. Then I changed from the old CLIQ to the Galaxy S, and all my "joined" contacts are now separated out again!
I'm thinking of just deleting all contacts on the phone, killing the T-Mobile directory on the T-Mobile site, then editing the GMail contacts until it looks the way I want it, then have everything sync back up again (except Facebook...way too much info for a 56 year old!).
Does anyone see a quicker, more streamlined way of getting my phone contacts the way I want them?
I figured mine out! The Waze Ap did it for me. What I had to do was go into settings and unclick the Waze ap from accounts, but ALSO in settings>Contacts to Display> I had the 'display all contacts' button checked. When I unchecked that all my contacts re-merged!! Whew. That was almost the last straw, I've been disappointed with the Galaxy S5, REALLY regret not getting the Motorola Maxx =(