This is has happened to me twice today. Our group beat the trainstopping alert with about 20 seconds remaining, and then the train still exploded. You need to make sure the clock stops running after the villain is dead. Not sure what Perfect World is having your devs doing besides ironing out bugs, but they need to stop it so you can properly QC your work.

In trainstopping, you also have to clear out all the subordinate mobs, not just the Supervillain. The other Smashes only require you to defeat the villain before the timer (or loss of citizens) ticks down. On more than one occasion, an enemy in Trainstopping has being knocked up to the higher plateau, unseen, or got stuck behind/in something, making it possible to miss them.

Of course, if you did that and it still kept ticking, then certainly. That's a bug.

The minions were indeed defeated prior to the villain being taken out.

Additionally, Trainstopping can be 'broken' by somebody defeating a minion before the mission itself stops due to how it doesn't count the defeat if it happens before the mission starts.

So if you see somebody charging up say a Sniper shot, bump into them to stop it.

This mission seems broken in other ways. I've failed this mission more often then defeated it, usually we spend more time trying to kill the goons then the villain. I don't seem to have to much difficulty with the other grab missions, but the goons in this mission seem to be too much.

Nope. Failed a dockside dustup today because one of the minions had a sliver of health left.

http://forums.champions-online.com/s...71#post2069771
The above is a link to a thread I started just over a month ago, bringing up just how easy it is to break this alert. This is probably what happened to you. I tested it just there when I saw this thread; still possible to break the alert in this way.
We should probably find a way to make this look as if this is a beneficial bug as that seems to be the only way to get a fix in this game.