It's probably because the game explorer only shows you the results for the target position as reached from the current position (i.e. it doesn't take transpositions into account) and only once you click on a particular move does it show you all results from the resulting position irrespective of how it was reached (those results, of course, having the same tranposition restriction though). The other results for 3...Bf5 that you see after clicking on it were simply reached via a different move order.
I think this is a pretty big flaw and it's been raised before but probably hasn't been made a priority in light of other large projects such as the Live Chess rewrite and the iPhone app.
I was just refining my slav defense, as one does late on a Thursday, and looking for the best response for black after...
1.d4 d5
2.c4 c6
3.Nc3
After 3...Bf5 there were 20 games in such a position, and 20% of them were wins for black.

When I actually play the move it says the win percentage is over 20% and there were about 100 games where that position was reached.
Have I missed something?