The warning never showed up prior though. Also that seems like an unfair difficulty spike.
My guess is that maybe a report was made at the exact same time the anomaly went off, which is very hard to do but may possibly be the reason for it to not show up or get overwritten at the wrong time.
My reasoning for it only popping up once per attempt is that the warning acts solely as like a 'wake up call' to tell you the player that they're missing things, if the warning goes off every time x anomalies are active it will 1) be too annoying and obnoxious 2) the player will be too reliant on using that system.