Minecraft 1.10.2
Forge 12.18.3.2316
Woot 1.4.0
RFTools 6.01

Crash log 1
Crash log 2

When I try to copy a Woot Mob Farm with the RFTools Builder (Shape Card) the game crashes as soon as I switch the lever. After rejoining the world the whole 11x11x8 area is filled with random Woot blocks.

I've managed to copy a Tier I with an extender and proxy, however that was unprogrammed and with no upgrades, so they were probably just treated as block. So I'll need to go back and test further.
I also need to read up on how the RFTools Builder works!

From your crash log both are Java casting issues where the Tile entity is of the wrong type. I'll just need to work out how that situation occurs.

I tried to copy a Tier IV with Upgrades. I tried removing the Extender, Proxy and Mob Controller though.