Don't use annotations, I think YouTube is going to remove the annotations feature. Instead use card feature. But I'm not sure about the "video is too short" issue. Just a suggestion. 
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That's strange. We suggest getting in touch with our Creator Support team, they may be able to help you further with this. Contact them here: https://goo.gl/BxLi8H . Hope this gets resolved!
Thanks. Twitter will use this to make your timeline better. UndoUndo
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