It happens because you probably play more in ones than others.
Example: imagine you have 4 chars, 1 of each vocation, all them have 12 hrs offline train now.
00:00 - You put them all to sleep right now
04:00 - You decide to log and play 2h in the ek and put it back to sleep
12:00 - After that, you login again, and see that the 3 chars trained 12h, and the ek only 10
Of course this is a extreme example, but sometimes it can be an irregular offline train time, sometimes we forgot to put some, various reasons. But, this is not a bug, just try to see how much offline train they all have. One tip is to put them to train everyday in the same hour, so the ones u don't use much can train the full 12h, and the regeneration takes 12h too, so you just need to put them once per day.