Here are some results where different CAS give conflicting results:

1. $\int_{y}^{\infty} \frac{e^{-x}}{x}{d x}$ for $y \in \mathbb{R}$ and $y>0$.
Wolfram Alpha [gives](http://www.wolframalpha.com/input/?i=int+exp%28-x%29%2Fx+dx+from+y+to+infinity) $$\log{y}+\Gamma(0,y)$$
and sage 4.7.1 gives $$ -{\rm Ei}\left(-y\right) $$

2. For all integers $n$, [Coq](http://coq.inria.fr/) proves $$n \mod 0 \equiv 0$$ and [Isabelle](http://www.cl.cam.ac.uk/research/hvg/isabelle/) proves $$n \mod 0 \equiv n$$ (The proofs are just stated in theorems, I can give the exact theorems if needed). Interesting, both proofs doesn't seem to lead to inconsistency though AFAICT they depict the usual _mod_.

_[Added]_ I am a fan of sage, but this bug annoyed me.

sage 4.7.2 incorrectly reports the girth of a 7 vertex graph:

    H=Graph([(0, 1), (0, 3), (0, 4), (0, 5), (1, 2), (1, 3), (1, 4), (1, 6), (2, 5), (3, 4), (5, 6)]) 
    H.girth()
    4
    H.is_triangle_free()
    False

sage 4.3 and 4.6.2 return correct value.

[sage session in the notebook and a plot of the graph](http://www.sagenb.org/home/pub/4102/)