1. Defence and National Security
As defence is a reserved issue the Scottish Parliament cannot do anything to stop or change potential laws on defence decisions. This is best exemplified by the war in Iraq.
The war in Iraq faced huge opposition worldwide and Scotland was not exempt from this- over 30,000 people have been estimated to march along the streets of Glasgow to demonstrate their protest over the war taking place. The war was not only strongly opposed by the people of Scotland- the SNP also fully backed up the decision to not go to war. However despite both the SP's and the people's best efforts, the war still went through, resulting in 179 UK casualties and over 500,000 deaths of Iraqi citizens.
Scottish troops died in a war which both the Scottish Government and people wanted to prevent. However, as defence is a reserved power, Westminster had the final say and overruled any other suggestions made by the SP. It is estimated that the biggest number of people had marched in Glasgow since 1990 and yet, it seemingly had no impact. Scotland couldn't prevent the death of its troops nor fulfil the wishes of the country and as such, it is obvious the SP is very limited in power in regards to defence.

2. Nuclear Power (and weaponry)
Scotland has no influence in regards to Nuclear Power. The current SNP Government is strongly opposed to nuclear weapons, nuclear power stations and nuclear dumps in Scotland. The Scottish Government's opinion on this matter has been backed by the Scottish Parliament which voted to support the SP's policy of opposing nuclear power stations.
Furthermore, in 2013 a YouGov energy survey concluded that Scots are twice as likely to favour wind power over nuclear or shale gas. Over 62% people in Scotland say they would support large scale wind projects in their local area- this is more than double the number who said they would be generally for shale gas (24%) and almost twice as much as nuclear (32%).
Moreover, despite the Scottish Parliament's and the Scottish population's opinions, nuclear weapons still exist in Scotland and still continue to cost the country £163 million per year in taxpayer money. 
Despite the fact that the government and the population are both opposed to an issue which costs them over £150 million per year, there is nothing they can do as it is a reserved power. The SP has no influence about something which costs hundreds of millions of pounds and is kept in their own country.