If you have such a problem here is how you can go about solving it.
Go to the Register reports > Sales > GST Summary for a given period
This gives a highly detailed report including this.
Now in trying to track down an incorrect GST amount divide the GST period into smaller units say months and check each month separately, do not worry about the time, our software is very fast and it will only take a moment, then divide a suspicious month into two and check each of these, afterwards the one that looks wrong divide into two and so on, until you find the day where the mistake is, then I check the transactions on that day.
