com.buuz135.industrial.tile.misc.BlackHoleControllerTile.BlackHoleControllerHandler.getSlots should be returning how many slots the inventory has, not the counts of the items within!

public interface IItemHandler
{
    /**
     * Returns the number of slots available
     *
     * @return The number of slots available
     **/
    int getSlots();

Black Hole controller provides that number to make available all the items provided by the black hole units.

I haven't looked is something is wrong but that's why it is coded like that. https://github.com/Buuz135/Industrial-Foregoing/blob/1.11.2/src/main/java/com/buuz135/industrial/tile/misc/BlackHoleControllerTile.java#L185

See the javadoc comment I quoted; the purpose of the function is to determine the number of slots, not items

Im not counting the items, The Black Hole Controller holds Black Hole Units (BHU) that have stored in the NBT a max Integer.MAX_INT of items. My getSlots() gets the number of items of each BHU and divides it with it stackSize to simulate how many slot would have.

Then perhaps your extractItem is wrong as iteration of the slots fails. See https://gist.githubusercontent.com/leagris/77c32db6e2519d9edf10ca10e5f837fe/raw/671effe58bb04a0e9f6e9aa5471cde0205c1a354/fml-server-3.log

That's another thing that could happen.

Yes it is . As I add extra slots as a buffer the last slots will throw an error.