The main issue with shooting in the darkness is the fact that when you have a dark scene it can sometimes be a challenge to get correct lighting. The issue comes when the one filming is trying to illuminate the subject that is being filmed.
This can be solved by using an illuminator on set or having the light on the camera when filming. Another option that may possible be considered is using well positioned spot lights so that the scene that you are trying to film is still dark but has enough light that you can still see the object and characters well enough to see what / who they are.
There can also be an issue when it comes to filming in darkness with the managing of the colour temperature, and this could possibly include the contrast.
A good example for where shooting in the dark has been done very well is in ' The Dark Knight Rises '
Many of the scenes are filmed in the dark e.g. night time , underground , tunnels...