There are a couple of general differences and one specific to the movie.
is being put back
This indicates an ongoing process—it's still happening. Also, the subject of the sentence is the money.
has been putting back
This doesn't necessarily imply that the process is still happening—only that it happened in the past. Sometimes we infer that it's continuing, but sometimes we don't. ("Up until now he has been, but no longer." "Up until now he has been, and he will continue to.") Also, the subject of the sentence is the embezzler.
As for the movie itself, Ben Affleck is pointing to account information that he's written on the walls of the room. For the sake of illustration, let's say he's pointing at a particular set of numbers and saying something in exclamation.
His phrasing should use a present tense in relation to that point in time—or a simple past tense.
"Look here! The money is being put back."
"Look here! He put the money back."
These makes sense. In the first, he means that at that specific point in time (that he's pointing to), the money is in the process of being returned. In the second, that's simply what happened.
But consider the more complex past tense:
"Look here! The embezzler has been putting the money back!*
Although understandable, it doesn't really make sense. He's pointing to a particular event which has no sense of real duration. So, there is no extended process in which it could have been happening
But this particular verb tense would make sense if he had indicated several different numbers:
"Look at all of these transactions. Do you see a pattern? The embezzler has been putting the money back."
Now, the use of the verb tense makes sense, because it's describing a series of events in the past that take place over a stretch of time.