On a general note, the unit cell is somewhat small in the XY directions, it will not be very expensive to add a bit of vacuum.
However, the main problem with the script is probably the use of Neumann boundary conditions in XY, which seems inappropriate.
It is basically impossible for the current to change sign unless the transmission spectrum is negative, so without seeing T(E) for each bias one cannot really advise further. My suspicion is that T(E) is basically zero at all bias values, but sometimes infinitesimally negative (which is never an issue as long as the real transmission is finite), causing the apparent negative current. However, with such a large value of the current in nA, that doesn't seem to be the case either...
Which ATK is this?