The main disadvantage of a subsistence economy is that if the system fails, and it can no longer meet the needs of those who exist within the economy, then it is difficult to obtain resources from elsewhere without currency. I'll explain in a bit more detail about this and other disadvantages below.
A subsistence economy is self-sufficient, and as such the economy functions in accordance to what nature can provide. What can be obtained through hunting, fishing, gathering, agriculture and what can be created from natural resources provide everything needed to sustain the community.
However, as a subsistence economy is wholly reliant on nature to provide for their needs, if a crop should fail, or their resources be damaged in some way, then they do not have access to alternatives.
The forces of nature determine how wealthy a community will be, and they have no control over the aspects which influence their assets. For example, they cannot make the rain fall if there is a drought.
Another disadvantage is that such an economy is reliant on the people who live within it.
If several members of the community were to fall ill, they may not be able to physically go and collect the things needed to meet their needs, but they could not go and purchase them either.
If they were to fall ill then they would not be able to pay for access to medical care either.
Being able to carry out the physical demands of a substance is vitally important to it's success. If not enough food is caught or collected, the people in the community will go hungry, and that's never good.