I generated an update installation wizard package from TDS containing my content, core db, and architecture (templates, etc). Syncing back and forth locally, I don't have any issues with how anything looks. However, this evening I deployed the UIW package to a server, and when I looked at some of the items, it was duplicating the rendering calls in the shared and/or final layouts. It definitely did not match up to what I had in source control or in my local environment.
We're using multi-lingual with language fallback, but I don't know why that would be causing an issue. This is with Sitecore 8.1 Update 2 and TDS 5.0.15.
Let me clarify the issue, since the comments so far seem geared toward items with different IDs. The actual renderings aren't duplicating, but some of the entries in the Shared or Final Layouts for the page layout are duplicating.
For example, we have a carousel container and two carousel slides locally, checked into TDS. We generate the update install package. When it's run on the server, there are now two carousel containers and four carousel slides. It's not consistently happening with every rendering listed in the layout, but they're exact duplicates down to placeholder and datasource.