Known Problems and Incompatibilities
NoCheat is a fairly complex plugin and heavily relies on knowing the games rules and predicting possible and impossible behaviour. It therefore may get confused by or into conflict with other plugins/mods. This is an incomplete list of such known problems with predictions about if, when and how they will be fixed, how you can avoid them, or how much you are screwed with your current setup, as it will never get fixed.
Players can't sprint
There is a 99% chance that you are using PermissionsEx and the ModifyWorld that comes with it, or CommandBin. Please read the instructions on ModifyWorld/CommandBin. It can prevent the server from seeing if players are sprinting (don't ask me why, that makes no sense whatsoever) if they don't have a specific permission node/the config file says so. Complain at the respective authors if you found that to be annoying.
Starting with v 2.16 NoCheat tries to correct those problems on the fly, if you have set the config option "debug.compatibility = true" in your NoCheat config.txt file.
NoCheat will identify flying players, but it can't reliably identify players that just hover in one place, not moving at all. Why? Well, CraftBukkit only feeds NoCheat with data if a player moves. A player hovering is a player not moving, therefore a player not seen by NoCheat.
Prognose: Likely won't fix. The situation may improve at some point, but it will never be fully fixed.
Getting kicked for Flying
You may experience at some point that you get kicked for flying, despite having the permission by NoCheat to do so. This is most likely the result of Minecrafts builtin fly protection, which will monitor and kick you if you fly. To deactivate this builtin mechanism (that doesn't stop like 90% of the fly mods anyway), you'll have to edit your "server.properties" file and set "allow-flight=true" in it.
Prognose: Just a misconfiguration. You can fix this yourself.
Towny and Flying
Technically not an incompatibility, but people get confused A LOT by this. So I rather write it down here. Towny has a "no-fly" feature builtin. So even if you have set yourself up to not be stopped by NoCheat when flying, towny may still stop you. Read their manual to find out how to turn off their feature, if you want to.
Prognose: Not a bug, nothing to fix.
Found a plugin that's problematic to use with NoCheat and think it belongs here? Has one of these problems been fixed? Tell me!