Simulating Pulse Induction Driving Circuit in Proteus Errors
I think I found the answer to both of my questions after messing around with the software and talking with a coworker.


The current probe requires that it be attached to a wire not the end of a component. IDK why this causes a problem but in all of my internet searching no one seems to have come across this error or if they have, hasn't posted it. Make sure when you apply a current probe that it is on a wire and not the end of a component as well as pointing in the correct direction.
I wasn't getting weird results for a couple of reasons. One was that by placing the MOSFET with source on the side of the inductor the switch was closing but the negative voltage generated by the inductor was pulling the source pin lower than gate causing the MOSFET to turn back on causing that slow decline in current and preventing the large flyback voltage spike. The solution was to switch to a P-Channel FET or move the N-Channel to low side switching.


Another side issue I ran into while correcting the MOSFET situation was that flipping the MOSFET so that the source was on the VCC side and the drain was on the inductor side caused a constant current to flow. What I overlooked was that the diode internal to the MOSFET was allowing current to pass from Source to Drain because VCC was greater than the forward threshold voltage. So again a P-Channel FET fixed my problem as well as moving to low side N-Channel switching.