In the above diagram, we can see that size should be relatively appropriate, and there should not be any rotation. This could be a false assumption. What we do not see is the game object hierarchy, in which our problem object could still be parented1 under another game object.
Should the game object be parented to another game object, you still want to observe the scale and rotation of any parents. Both of these will be multiplied by local values, in order to give world values. World values are what really matter, in context of the error being displayed.
In this case, I believe this could point to additional rotation. You say that the circle collider works fine - this would not be the case, if world scale really did make the game object too small.
However, as discussed on the Unity Answers site, the box collider can still throw this error as it approaches 90 degree rotations. This is because the rotation converts to a skew in the interpreted size, and at 90 degrees, one of the axis is going to be approaching rather minimal values. As the error reports, we can't have that.
Ultimately, if this is the case, you need to figure out if you need the parent. If you do, in turn, you should decide if you need rotation. If you need rotation, you should use a circle collider, instead.
Failing all that, due to the precise nature of your problem, I would honestly put this down to a Unity bug.
1 It occurs to me that I have missed the additional note that there is no parent, but it is still worth addressing the code where you instantiate objects. You can set a parent during instantiation without it visually displaying so in the hierarchy. I'm unsure why such a method would be useful, as it took me some time to figure it out, too.