The InventoryHandler method public boolean addOutput(@Nonnull ItemStack stack) can cause issues if the provided ItemStack has a count of more than 64 items. The issue is that NBT data cannot save ItemStacks that are bigger than 64. This could happen for example if someone edits the config for the productivity upgrade to a high number.
The solution would be to split the stack in parts smaller than 64. I am working on a fix for this issue in my fork

Here is a link to imgur showing the buggy behavior