The implications of these lapses can lead to departments not being able to fully deliver on mandates that the ministers and the Prime Minister have given them. For example, if they are not able to fully spend in some specific areas, it may mean fewer land claims that get settled, or it can have impacts on the delivery of health care services to some communities. These are all hypothetical, of course.
Lapses may also mean that departments asked for more than what they really needed, so it does not necessarily mean that it's a bad thing. Personally, as a taxpayer, I'd rather have government departments not spend just for the sake of spending if they don't need all the funds that have been allocated to them. However, it may indicate a mismatch between what government departments planned on spending and what was realistically achievable.