Unfortunately, I can't remember any maps where this would be easy enough to reproduce.

cs_estate for example?
This table is a func_pushable: http://image.noelshack.com/fichiers/2013/05/1359720249-cs-estate0003.png

Steps:
Round 1 : Move its origin. Then kill yourself.
Round 2 : Its origin is now wrong ( Imagine if someone push it on a CT/T Spawn ... ).

@micapat Good catch, additionally, if you destroy that table, it will be gone forever. BUT you still will be able to move it around, while it is invisibile.

@alfred-valve I made a map to demonstrate func_pendulum and func_plat: removed

How to test pendulum: go under one of the pendulums, so it gets stuck for a while, restart the round and see how they are out of sync now.

How to test plat: press the button behind the spawn point, restart the round.

func_door / func_door_rotating have a little problem too. Here is a example:

1. When the map is loaded, the door starts closed, and can be opened/closed only with a button ( Note: I take a example with a button, but I guess that even automatic doors have the same issue ).
2. You restart the round. Nothing happens ( Normal, the door is closed ).
3. You press the button ( And so open the door ).
4. When the door is opened, you restart the round.
5. When the new round starts, the door is opened, and starts to close itself. <--- Here is the issue.

With this map, you can make this test: http://www.sendspace.com/file/kgcjo1

It will be better that the door is totally reset ( And so starts closed in this example ) each round. Indeed, on some maps, the speed of doors is really slow, and some players can access to some areas that they shouldn't in the beginning of the round.

Thank you.

I forgot the entity func_tank too, when the flag "Active" is set ( To make a sentry which attacks automatically all players for instance ). If you deactivated it, then it will not be reactivated in the next round.

With this map you can see this problem: http://www.sendspace.com/file/0xkaxq

@xPaw: You talked about the entity func_plat, but is there the same problem with the entity func_platrot too ?

@micapat Probably.

@micapat If the bug is fixed, that a door with "x use only", "x starts open" and "delay -1" can only be triggered once a round, many maps won't work anymore, because this bug is used to give the door the name "game_playerspawn" and make a reset trigger which can only be triggered once a round, to reset entites at a round start for example.
trigger_once unfortunately does not work. Anyway, many maps wouldn't work anymore.