If you are entering these expense in the Employment Expenses section or the Self-Employment section, then the amount you can claim is based off of the number of kilometres you drove for employment/business purposes.

Since you only used your car for work purposes for 3 months, you can use the information from your logbook to determine what the total number of kilometres you drove during just that period, and use that instead of the total kilometres for the whole year. Enter the kilometres you drove for work and your expense amounts for just those 3 months. The program will calculate what portion of the expenses you can claim.