I'll be curious if anyone has a good answer for this. Googling around, that message seems to happen to a lot of people, and there's no definitive answer why, or no solution saying "it's caused by X and can be solved by Y."
It may be simply RAM related, both how much the computer has and how much you allocate to Java when you launch MinecraftEdu. It may also have to do with having other processes running at the same time? I'm really not sure, but most threads talking about it say something to the effect of "if your players aren't complaining about lag, you probably don't have to worry about the message."
I've seen it on every server I've run.