The objects are constructed of a number of circle shaped Box2D bodies (hereafter deform points) connected together by distance joints which allow the object to "deform" when the deform points move around. Collision works more or less fine when the objects are colliding with other standard Box2D rigid bodies such as a box polygon (what they're sitting on):
The problem starts when two soft bodies collide. As you can probably guess from the way they're constructed, the two often pass through each other since the deform points for which Box2D handles collision are small and spaced apart, so they easily don't collide when the two soft bodies should. If the two bodies are placed like seen on the left in the following image, the circle passes through the square, rather than bouncing off the top of it as it should:
I've tried solving the problem (methods shown below) by tessellating the bodies more so that the deform points are closer together (left), which seems far too resource intensive and didn't affect much anyway. Then I tried enlarging the size of the deform points to fill the gaps (middle), which worked perfectly for the collision but as you can see caused problems mapping the texture to the object since the textures don't appear to collide. After that I tried to bound the outside of the object using polygon bodies connected between deform points using revolute joints, this works with the texture better and does prevent objects from falling through each other, but it stops the object from deforming properly.
I can't think of any more ways to tackle this problem, but I'm very new to Box2D and libGDX and maybe I'm overlooking a much more simple solution. I'll give any ideas a shot.