Yes, there are inconsistencies, but they are for the most part tolerable ones. It is perhaps a moment that stretches credulity when the Doctor puts his hand into a crack but it is not bad drama for all that when he pulls out a damaged piece of the TARDIS (from the future).
Making a quick list it is easy to see that a crack behaves something like a window. You can i) see and hear things (at other places and times) through a crack ii) you can pass things (across space and time) though a crack iii) you can be sucked through a crack (think decompression) and cease to exist or be remembered having had every trace of your impression on spacetime removed and perhaps iv) you can make your way from one place and time to another by passing through a crack. The Vampires of Venice episode seems to allow for the latter possibility with the vampires (i.e. Saturnine creatures) having fled through a crack that permitted their escape to Earth from some terrible threat that they labeled "the Silents".
The strangest thing witnessed in connection to a crack is when in the Cold Blood episode a white light envelops Rory's dead body as it is drawn into a crack (as seen from where the Doctor and Amy stand). There apparently is something non-random and intentional happening here, but it is unclear whether we are looking at a form of technology controlled from the other side of the crack or whether some entity is able to use energy from the crack to achieve certain ends. Rory's reappearance in The Pandorica Opens as a self-aware individual (albeit Auton) who remembers everything about Amy and the Doctor is incredibly strange, so much so that the Doctor labels him a miracle, something he says he has never seen before. The way these elements are connected is unclear but it is reasonable to suppose that a connection exists.