I was just able to accidentally get two different Button object styles in the same theme with the same name "Conflict_Button" - see screen shot attached.
OS X 10.10.5, FileMaker Pro Advanced 14.0.4, local file created in FileMaker 12 or 13 - theme originally created in FileMaker 13, the style in question created in FileMaker 14.
I just had this issue, and haven't had the time to try to reproduce it etc - I thought I'd see if it's a known issue before I spend time on that.
This solution consists of a few different files. The file I got the issue in (File1) had previously been duplicated to create File2. In File2, I had added the button object style Conflict_Button and created objects for it. A few days ago, I had copied some of these objects from File2 to File1, to two different layouts, but not saved the style information as a new style, so that it was Default + LocalCSS.
Today, I wanted to clean that up and saved the button object on Layout 1 in File1 it as a new style, named Conflict_Button as in File2. I flipped to Layout 2, realized I hadn't saved the changes to the theme, flipped back to Layout 1, saved to them, and then back again to Layout 2, where I now saw this odd case of two styles with the same name, with the Theme having unsaved changes.
If I go back to Layout 1, the Theme has no unsaved changes and there is only one style called Conflict_Button.
After reverting the changes to the Theme on Layout 2, I only see one Conflict_Button style, but now with unsaved changes.