A very late answer, but could be useful so...
I just had almost the same problem using Xcode 7.2. For me there were two steps to resolving this issue:
- Read the Xcode error message carefully to find out which Contents.json files are affected -- at the very least the message should include the names of the images affected (at least it did for me), then you can browse the Assets.xcassets folder in the Finder and locate the relevant image folders. Each image folder will also contain a corresponding Contents.json file. Remove the conflict from Contents.json files as described in 22076517.
After doing this, I found that although there were no more tree conflicts, I got a warning that a single Contents.json was still being reported as conflicted. So, on to step number 2!
- Remove the offending image folder to a safe location (anything that points to that image will throw up a warning or error at this point, so try not to panic!), clean the project (not sure if this is necessary, but I find that doing this regularly lowers the chances of random, strange build errors), and then put the files back and recommit them as though you just added new files.
And that resolved this issue! Good luck.