Virtual Combat Cards has been design trying to make it resistant to problem, so that you don't lose you combat. Eventually a bug might popup and may cause it to stop it's normal behavior. If this happens please report the bug, but don't panic there are ways to recover you combat.
The internal tracker is quite resistant to problems, and most of the times you should try the following before giving up:
If all fails, take a screen-shot of the combat sequence and the logs, and open a bug report.