This commonly happens when the server is being hosted on a computer and someone is trying to play on the server, form that computer at the same time. The best way to prevent it is to run the server nearby from a different computer or server box. Connection speed is also important. Try using an ethernet cord on your computer when playing minecraft instead of wifi/airport mode. Ethernet is faster. The amount of RAM allocated to the server also plays a major role in game speeds.
There isnt any specific problem causing this, just general lagg. Here are a few plugins that can help reduce lag a little:
Another common form of lagg on a server is map size getting to large. You might want to consider getting a worldborder plugin.