4tesQ said:

Since starting the game, my skull runes have been steadily decreasing without me using them for anything. Just this past week I’ve gone from 30 to 25 to 20 and now down 2 more since this morning. I thought skull runes only get used when you apply them? I have not been attacked and I can discover no information on this anywhere. Please advise. 

it shouldn't be decreasing on its own and neither it can be taken away by some enemy castle. Just cross check again if you are not mistaking them with red soulstones. 

 Please contact support.