I slept rough myself for a while, and was lucky enough to get help before it because a long term life style.
Challenges? Well, resources, mainly, but there are others.
Security is a constant challenge.
There are two basic types of shelters, the ones that take anybody, and the ones that are invitation only.
The invitation only ones are a step into getting back into long term housing, of some description, and residents need to demonstrate certain standards of behaviour, or they lose their place. This leads to a certain number of disgruntled ex residents, and arson is my main fear - it doesn't happen often, but it does happen
Challenges with the residents - most residents want help, and will accept it. There are problems that are very deep seated, and not easily undone though, such as alcoholism, or behaviour which can be destructive. The most common type of behaviour I see that is destructive is a kind of love and generosity for the whole world, sharing everything with everyone, letting anyone in to your secure accommodation, lending anyone your tiny amount of money if they ask for it - no boundaries, judgement or discernment. This is the result of a form of attachment disorder in childhood, and is strangely incompatible with modern living! This is probably more common than alcoholism in my experience, and just as difficult to resolve.
There are other challenges, obviously, but these are the ones that spring to mind first