I've just checked the sitemap and it's no longer duplicating those links.
So one of the add-ons is at fault.
Could you list all of your add-ons? You can re-enable the add-ons now too if you haven't already. Once you have re-enabled them all, if you can also screenshot your Admin CP > Options > XML Sitemap page options that would be useful too (there may be another add-on not extending the sitemap system properly perhaps?).
Nice. Here is the list of addons
"Stay Logged In" checked by default 1.1
About Me by Waindigo 1.0.2
Add Account Wrapper to Conversations 1.0.1
Add Poll to Existing Threads 1.1.4
Add-on Install & Upgrade 1.1.1
Alphabetical Pagination by Waindigo 1.0.1
AutoComplete Combo Box by Waindigo 1.0.2
Bookmarks 1.3.0
******* - Auto Close/Move/Delete Thread Inactivity 1.0.1
******* - Conversation Live Update 1.1.0
******* - Credits Premium 1.6.3
******* - Custom Node Style 1.2.0
******* - Metadata Essential 1.6.2
******* - Most Followers Member 1.0.0
******* - Prevent URL Profile Post 1.0.0
******* - Thread Live Update 1.1.1
******* - User Profile Cover 1.2.5
Control "nofollow" URLs 2.2.3
Discussion in Resource Overview by Waindigo 1.0.1a
Double Post Merge 1.0.9
Email Alerts by Waindigo 1.0.5a
External Accounts Extended 1.6.0
FAQ Manager by Iversia 3.2.0
Followers Count 1.0
Forum Moderators 2.5
Inactive Members 2.5
Increase Newest/Highest Posting Users 1.0
Info Tab 1.0
Latest Members Block for XenForo 1.2.x 1.0.1
Live Feed 1.2.1
Live Update 3.0.1
Login As User by Waindigo 1.1.9a
Lost Password by Waindigo 1.0.0
Most Online User 1.2
New Users Welcome 1.2.4
Newest Post First by Waindigo 1.0.3a
Nodes As Tabs 1.2.2
Notifications 1.7.6
People You May Know 1.0.2
Post As User by Waindigo 1.0.7a
Post Ratings 1.6.6
Profile Completion Steps 1.0 RC2
Profile View Count 1.3
Register Email 2.0
Registration Form Timer 2.0
Reset Password From ACP 1.0
Resource Count in Message User Info 1.0
Resource Count in Visitor Panel 1.0
s9e Media Pack 20140920
Show Similar Threads On Thread Creation 1.1.7
Similar Threads 3.3
Social Connect (Bundle) 2.2.5
Start Conversation from Post 1.2.5
Sub-accounts by Waindigo 1.0.9a
TaigaChat Pro 1.3.0
Template Modification System 1.3.1
TinyMCE Quattro 2.4.1
Top Posters Sidebar 1.0
Trophies by Waindigo 1.0.5a
Trophy List Overlay in Visitor Panel 1.0.0
Undelete Users by Waindigo 1.0.3b
Unread Post Count 1.1.3
User Banners on Member Cards for XenForo 1.2.x 1.0.0
User Criteria by Waindigo 1.0.13a
WDB Popular Content 1.0.5
Wuebit.com Twitter Profile Addon 1.0.2
XenCentral Ad Server 1.3.3.1
XenCentral Framework 1.3.4
XenForo Enhanced Search 1.1.1
XenForo Resource Manager 1.1.4
XFA - Better Blogs 1.0.40
[8wayRun.Com] XenAtendo (Events) 1.5.0
[bd] Keyword Alert 1.0.4d
[bd] Tag Me 3.0.5b
[bd] Widget Framework 2.5.9
[Extra LIcense] Unread Threads Counter 1.0.1
[MWS] Daily Statistics 1.2.4a
[Nobita] Social Media 1.1.0
[Nobita] User Preview 1.0.0
[Nobita] XenForo Alert Plus 1.0.7
[RainDD] Thread Activity 1.0.2
[SurreyForum] XenKingDir - Business / Links Directory 1.2.0.8
[Tinhte] XenTag 2.1.0
[WGBB] Daily Post Count 1.0.3
screenshot admin sitemap options