As I was trying to reproduce your problem, it seems that I never
tried to print with only one material loaded in the Ultimaker3...
The
Ultimaker 3 knows when filament is loaded in an extruder (especially if
it was loaded through the "load material" routine of the printer), and
the profile for this machine currently provide material information for both
extruders, even if we only use one.
In addition, Ultimakers use comments to setup some parameters for the printing (like temperature, chosen material, build dimensions, quantity of used material, etc) instead of using normal gcode, like many other printers, so it's normal that the problematic lines were comments.
Nevertheless, you might be able to click on the "Ignore" button on the error message displayed by the printer, especially if you sliced with the default settings (by default, everything is sliced to use the first extruder of the machine - the one one the left - , so assuming that you've loaded filament in this extruder, it will print fine).
In a near future, the profile for this machine might be revamped to feature a smarter way to manage both extruders, and to prevent this kind of errors.