Items like the PneumaticCraft wrenches cannot currently be removed from the network inventory again.

This might be related to the airhandler cap they are using or item caps in general.

In terms of PneumaticCraft this is caused by ItemPressurizable having different NBT values between the server and client (see ItemPressurizable.java#L115-L128)

There is probably no straightforward fix at all currently possible.