Gaps are empty cells between cells containing lectures or bookings. If you have selected [x] Assume bookings as lectures (when counting gaps) in Options|Timetables, also bookings are considered as lectures when gaps are counted. When optimising the timetables, the number of total gaps weighted by their category is the criteria that is minimised. In Timetables view the indicators show the change of the number gaps in timetables if the assumed action is taken.
Note that the number of gaps is not the only criteria for a "good" timetable. When timetables are created automatically, minimising the gaps is the goal function, but there are also additional restrictions user can apply. See details in Optimise.