Fixed-term Parliaments Bill

Perhaps I have this wrong, but my understanding of the present position is that the Government may be defeated on a serious matter such as whether to go to war and may take the view that it is not a confidence motion. However, in such circumstances, the leader of the Opposition would table a confidence motion, which takes precedence over all business. If there is an argument about whether the issue is a confidence motion, it is up to the Opposition to bring forward a confidence motion on which there will be a vote, so why is this such a big problem?