There are two types of cancellation: there is the substitution type 'cancellation' and the <Cancelled> button in the substitutions window.
The 'Cancelled' type designates a lesson where there is no cover for the absent teacher and which is therefore cancelled. You specified in the substitutions time grid when cover should by default be provided and when periods should be cancelled. It is therefore possible that certain lessons are set to 'cancelled' immediately after an absence is entered.
The <Cancelled> button allows you to change any open (i.e. not yet processed) and any already processed substitutions to 'cancelled'.