At least one recent study suggests that the longer the stem cells hang around undifferentiated in vitro, the greater the chance of them turning cancerous in vivo.
Unfortunately, I don't have a link to the article I read. I believe it applied to both embryonic and non-embryonic stem cells used in animal studies.
Yes, the same is basically true of any cell that you culture outside of the body. We don't necessarily know of all the growth factors they need to group and develop properly. Also, we are putting them under selection pressures that favor cells that divide rapidly. Manipulation of the DNA damages it in often unintended ways. By the time you put it back into the body, you really have changed it in many ways, many of them undetectable. And you can't really practically sequence its whole genome before you do, to make sure that you've only changed the things you wanted.