Why do motorcycle engines have a random displacment?

The ninja 250 was technically 248cc. The Honda cbr300 is 286cc. There are plently of other examples too. I've never seen a bike whose engine is actually what they advertise

It's not 'advertising' and it doesn't just apply to motorcycles.

The "6.2 liter" engine fitted to a 2015 Chevrolet Corvette is actually 6,145cc.
The "5.2 liter" engine fitted to a 2015 Ford Mustang is actually 4,940cc.
The "5.7 liter" engien fitted to a 2015 Chrysler 300S is actually 5,654cc.

All manufactuers do it - it's called 'rounding up'. Very few engines, whether in cars, motorcycles, trucks, vans or big rigs, are exactly the same displacement as the name suggests. Things other than your delicate sensibility to numerology drive engine design: evolution from previous designs; use of available parts (pistons, etc.). But I'm very, very sorry that you are offended. Advertise, that's the key word. What sounds better, the Ninja 250 or the Ninja 248? Because bores and strokes are measured precisely, often in whole millimetres, however that means that cylinder volumes which rely on Pi (3.14159) do not tally to whole numbers. In competitive motorcycle racing motors are limited by displacement class. The class limits are round numbers, 250, 300, 600, 750, 1000. The motorcycles are slightly lower displacements in order to not be disqualified and bumped up to the next larger competion displacement size. If you were racing in a 250 cc class and by engine wear your bore size wore and was measured as over 250cc, you may be removed of race title and prize money.

Things other than your delicate sensibility to numerology drive engine design: evolution from previous designs; use of available parts (pistons, etc.). But I'm very, very sorry that you are offended.

Advertise, that's the key word. What sounds better, the Ninja 250 or the Ninja 248?

Because bores and strokes are measured precisely, often in whole millimetres, however that means that cylinder volumes which rely on Pi (3.14159) do not tally to whole numbers.

In competitive motorcycle racing motors are limited by displacement class. The class limits are round numbers, 250, 300, 600, 750, 1000. The motorcycles are slightly lower displacements in order to not be disqualified and bumped up to the next larger competion displacement size. If you were racing in a 250 cc class and by engine wear your bore size wore and was measured as over 250cc, you may be removed of race title and prize money.