Thanks to Yarik Halchenko for this explanation.
Imagine a series of commits A, B, C, D... Imagine that there are two branches, topic and master. You branched topic off master when master was at commit ‘E’. The graph of the commits looks like this:
A---B---C topic / D---E---F---G master
git diff master..topic
will output the difference from G to C (i.e. with effects of F and G), while:
git diff master...topic
would output just differences in the topic branch (i.e. only A, B, and C).