What does the warning 'The entered timetable is probably not complete' mean?

By default the software tries to create a timetable for each class that starts with 1st lesson. It also calculates the average lessons per day and tries to balance the lessons put per each day.

However if your class has less than 3 lessons per day, the software assumes that this is a special class and turns off the automatic teaching block for this class.

So it's lessons do not have to be from 1st period, they can be at any time during the day.
For example: the lessons of class 5.C on the picture can be anytime during the day.

You can ignore this warning message or if you want to get rid of the warning message you can specify that this class shall not use automatic teaching block calculation: