I just went through this yesterday with the stock hot end. There is some misalignment between the extruder lower opening and the hot end heatbreak opening. The manual says to put an M3 washer between the upper block and the motor which is required for alignment. I also found there is some side to side slop in the holes that must also be accounted for.
What I did is to put a small allen wrench through the filament path. This held the parts in alignment and then I could complete the assembly. I also went through several washers trying to find the right thickness. But once I could tighten the assembly and the allen wrench could be removed easily, then I knew it was good to go.
After that I inserted filament and it entered the heatbreak easily.