You may be encountering ‘floating-point approximation error’, explained in: Why is 0.3 - 0.2 - 0.1 (or similar) not equal to zero? (link).
If that’s the problem, use a tolerance with find:
Y = [1 2 3 0.0001 4 5 -0.0009]'
Zr = find(abs(Y) < 0.01)
Zr =
4
7