You normally gain prestige through battle but i habe only been gaining honour. Am i doing something wrong?
If the battle is close, and especially if it's big, you'll get guaranteed prestige and honour.
However, the more one sided it is, the less of a chance you'll receive Prestige/Honour.
Remember that prestige is much harder to gain than honour. Fighting a group of monsters or undead alone will probably get you at least 1 prestige.