The basic rule to manipualte a market is to make sure supply is short, so you can control it. So it's easily done for rare items, items with a very high demand, or isolated regions.
Have a look at the amount of buy / sell orders, and the average number of items exchanged per day in the region. If there is a lot of activity, the market may be controlled, but it 's unlinkely. It would require a lot of accounts with a hefty sum of money, and may not be worth it.
In not-so-populated areas, a good sign of the sudden arrival of someone who wants to manipulate a market is the extremely sudden augmentation in sales. It can generally points to someone arriving and buying all the sell orders so he can control the supply in the region.
This is far from being exhaustive, but as a rule of thumb, long-term statistics are defintely your friend here. If you see unusual patterns, there might be something going on.