For a proper answer wait till a sailor or navigator comes along ...
Charts used to plot a course have north at the north pole (true north). On a compass, north is magnetic north, which is off to one side of the north pole. When you plot a course you have to take the difference (deviation) between true north and magnetic north into account.
There are other things which can affect a compass too ... metal in a ship, the engine, local magnetic field variations, electrical equipment. These cause other deviations and the compass is adjusted to correct them to some extent. Still, it is possible to draw up a table of deviations which are related to the ship itself.
Basically the conclusion was that, even allowing for these deviations in the compass readings, the course laid out for the ship was neither safe nor reasonable in the circumstances. Or to put it another way, if someone was daft enough to lay out a course which took the ship too close to shoals, rocks, wrecks, sandbanks and the like, while disregarding the effect of wind and currents (no GPS to tell you exactly where you were back then), that person was going to be suffer the consequences.