When there's a block above the wolf, the wolf - tamed or not, won't be able to see skeletons standing right next to them, while the wolf is in the minecart. It takes having a partial block over them with the opening toward the skeleton for the wolf to see and attack the skeleton. I tried glass in the picture below, but still to no avail.

In previous versions, the wolves have no issue at all with line of sight considering they were able to see the skeleton's feet.