When your empire gets large you can't help but get these vices... its the AI's way of making things difficult.

Plus you would expect a large level of corruption in a successful Empire.

I would sugguest you lower taxes, but that probably won't do it since I have had bad trading vices come up even on Very low tax levels.

Some provinces also seem more prone than others, unless its my imagination. Muscovy always seems to breed bandits and theives year after year, afterwards I had to face facts and just leave them in power

Lowering the taxes may help, but then again it may not... when in doubt resort to assassination, stripping them of their titles, framing them for treason or burning them