I also encounter the same issue.
It is not an issue that you loose a plundering, It is rather that there is sometimes a timing issue, and the timers indicating the time left are not accurately updated. I think if you manually attack, that the timers for the 5 opponents get frozen, and that if you return from figthing, that those timers continue to run based on the time left before you start to battle. if you enter the city to plunder the new data from the server gets loaded. But it will not have any impact on the faulty counter. So below you can see that you still have time to plunder but the cityview only allows attacking or aiding.
If you just load the next 5 opponents and then get back to the previous opponents, then I think the counters get updated. so you don't have to load the whole game.