Custom Crafting station doesn't work as intended

Break will exit your loop, not the if/else condition. This means it is only running once.

Your current logic looks like this:

repeat 9 times
{
	if( it's a potion ingredient )
	{
		if( water breathing ingredient )
		{
			Put bubbles in slot
			Jump to @OUT
		}
		else if( poison ingredient )
		{
			Put skull in slot
			Jump to @out
		}
		
		if( tagged with potion effect )
		{
			move to next effect slot
		)
	}
	else
	{
		move to next ingredient slot
	}
}
if( not a goop ingredient )
{
	clear effect slots
}
@OUT

What you want is this:

repeat 9 times
{
	if( number of items in slot > 0 )
	{
		if( it's a potion ingredient )
		{
			if( water breathing )
			{
				put bubbles in effect slot
				move to next effect slot
			}
			else if( poison )
			{
				put skull in effect slot
				move to next effect slot
			}
		}
		else
		{
			clear effect slots
		}
	}
}

more test

I'm not able to edit the post above, ignore the 'more test' at the end and maybe add a 'move to next ingredient slot' at the bottom (inside the repeat)