How to reproduce:
Create a LP Network, in it create the following crafting recipe:

Cobblestone to Stone with a furnace
Stone to Stone Bricks in the Logistics Crafting Table
Then, create an AE2 network, in it put 4 cobblestone and 4 stone.

Link LP to AE2 and try to craft 4 stone bricks via the ME Terminal.
The ME Terminal will open this page:

As you can see he says that he need 4 cobblestone, even if it already has 4 stone. Then when you press "Start" the AE2 will craft everything normally (Putting the stone into the Logistics Crafting Table).

The crafting works correctly in every case I tried (Missing stone and not) but the Crafting Plan doesn't correctly show what he's gonna do.

And I can't craft stone bricks if I haven't got cobblestone even if I have the stone that the craft needs.

In the latest update 1.3.1 I added the option to toggle between the new and old bridge logic. Shift right clicking changes the mode.

Unfortunately AE doesn't give me how many it wants to craft, so I can't calculate with it.