This has happened to me twice. I am playing as veteran, I use my first two alerts and I alert a third night but change my mind. It is verified in the log that I have changed my mind, but the next night I have no more alerts left. This is on PC through steam.
The "changed your mind"-message is triggered client side, thus it doesn't mean the message got sent in time. Latency can be quite an issue in the game depending on your location. This is not a bug, I apologize.
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