The majority of all server issues are due to either plugin errors/incompatibility or world corruption. There are three main steps in locating and troubleshooting any issues you may be having with your server:
1. Check your server console, server.log and any crash reports for errors. The server.log is located in the "root" directory and crash reports are located in the "crash-reports" directory via FTP.
2. Set your server to the default vanilla Minecraft jar and check your world for corruption. If you do not find any errors then the issue is likely plugin related.
3. If you see plugin errors in any of the previously mentioned locations, you need to disable those plugins and check the console to see if the errors have stopped. If you are not sure which plugin is causing the error, you should disable all plugins (this is done by simply removing or renaming the plugin's jar file, you do not need to remove the folder). Then reenable them one at a time while checking the console to find the culprit.