So is the common problem with dual extruders one extruder leaking on the print or misalignment with one nozzle higher or lower than the other?
yes.

You basically have to build a wall around the print and for each layer and colour change it empties both nozzles before printing.

I reckon it takes 2-3 times longer than a single material print.

One reason I almost never bother.

Plus there's the whole two seperate but interlocking stl files to deal with :-)