Well, rigid in this context means "doesn't deform in any way." Every point within that body remains at a fixed position relative to all the other points, and these relative positions don't change. This is an idealization. There is no such thing as a rigid body in real life.
If I had been answering your original question, I would have cited air resistance (drag) as something to be looked into. I.e. you are not dropping this thing in a vacuum, and therefore gravity is not the only force acting on it.
More importantly, for what height and time did you make the measurements?
The oscillations of the balloon and the approach towards the terminal velocity (When the velocity is at the terminal velocity, the balloon will no longer accelerate) could have immense impacts on the average acceleration, flooring its value if you take a measurement over a long enough time.