So, Update. I extracted the Subtitle from the 2D Version of the Movie and copied into the Movie Folder. Kodi found it. I don't know why, but there is a timeshift between the displaying Subtitle and the runtime of the Movie, but that doesn't matter. The Subtitle was displayed only once and not twice.
BUT: i had another Idea. I have another little HTPC on which i was running Kodi before i switched to the Raspberry. I switched because the Raspberry had several Advantages like less power consumption, less noise but the most important thing was, the Rapsberry was able to switch the 3D Mode of my TV which my HTPC was unable to do. According to the Forum is this an issue of the Intel Driver. After testing with the installed Jarvis (no issues) i downloaded the newest Generic.x86_64 Libreelec Image, made an Update to Krypton and tried to play a 3D Movie with the 3D Subtitles. And guess what.... It doesn't double the Subtitles...
Short Summary of all my testing:
Raspberry Pi2 with Isengard and Jarvis: no issues
Rapsberry Pi2 with Krypton: double Subtitles
Intel based HTPC with Jarvis and Krypton: no issues
Can someone explain that to me? Is this a bug on the Raspberry Image of Libreelec?
Edit:
Just hooked up my Workstation PC which is running the Windows App of Kodi. Same thing here: No doubled Subtitles.