A strange matter happened to me, there was 10K+ crown lie on my repository and half of them disappeared when I log on again. I m sure I didn't use them in supply depot or bidding. The last bid was yestoday and cost approximately 500 crown. All of things I did today are just farming for token and didn't buy anything with crown, but they just missing.
So sad because that was my effort I did, I don't even know the reason why they lost
I'm not aware of any bugs in the game that lead to loss of crowns. Probably you spent the crowns and forgot. For example, you crafted a 5-star item, which costs 5,000 crowns.
If you really think that you should have these crowns, contact Support. Good luck.