Currently, by default, the submission system does not distinguish between branches, tags or revisions of a project that is to be submitted to FigShare.
Most development teams take advantage of branches to isolate releases and development branches (see A successful Git branching model).
In regards to this, my humble suggestion is to list tags and branches in a project whenever a user initiates a submission. This way people will, for example, able to say: "I want my latest stable code to submitted to FigShare", which provides incredible flexibility for submissions and this model will better with the current established development strategies.