The reason is a little arcane: negative zero:
The other answers and comments are wrong: this has nothing to do with floating point error or "almost zero" values.
The second column values are exactly zero, and we know that the value is exactly zero because in both long and short format only the exact value zero is displayed as one single digit "0", just as all of your examples show.
So what is the catch?
The catch is simply the IEEE 754 defines two zeros, a positive zero and a negative zero. Same value, different signs. Some (but not all) operations retain the sign when operating on them.
One of your zeros is negative and one is positive, but unfortunately MATLAB** displays them without the sign:
Y = [0;-0] % positive and negative zero!
X = [-0.95;-0.95]; % these values are not really relevant
atan2(Y,X)
Here is a useful trick to detect if a zero is positive or negative (simply displaying it doesn't work):
Y % they look the same ... but are they?
sign(1./Y) % no!
Negative zeros can be generated by some arithmetic operations, or perhaps by converting data from text. If you want to remove negative zeros from an array without changing the sign of the other data, just add zero:
Z = [-0,-2,+0,3]
sign(1./Z)
Z = 0+Z % remove negative zeros
sign(1./Z)
** for what it's worth, Octave does display the sign.
