Why has my honeycomb toffee set in layers?
It's normal for some layering in home made foamed sugar (hokey pokey, honeycomb etc.)

The problem is that you can't stir it quick enough to get an even distribution of acid to alkaline (the bubble making process) throughout the mixture before it cools to the point you can't stir it

Factories use fancy heated augur style stirrers to avoid this, and they don't make domestic sized machines like that

Mixing in the alkaline while the pan is still on the heat. Mix fast and carefully with a rubber spatula so you can get into the corners on the pan, and then scrape out with the same tool. Time is very short

Make sure you acidify the sugar (a tsp of white vinegar will do). Carefully sift the alkaline powder a few times, and make sure you add it to the pot evenly, not in one big lump

Also, adjust the recipe acid and alkaline quantities, you may have insufficient to fully react with the quantity of melted sugar?