I have magnolia tree which has produced some seed, when should I sow them?

Sow the seed as soon as it is ripe, generally around October.

Sow them in an open-textured compost and place them in a cold frame.

They will take up to 12 months to germinate.

Pot on as soon as they are large enough to handle and grow on for a couple of years until they are of a size suitable to be planted out in their permanent positions.

My Magnolia stellata bush flowered well in spring! and it has also produced a few flowers in September, is this unusual?

Magnolias can often produce the odd flower out of season so this is not unusual.

Similarly, there is no reason why your plant should not flower normally next spring.