I typically make most of my changes mid-match, including changing players roles (although that doesn't happen as often). In this case, I made some slight adjustments including dropping my RWB back to a RB to mark the opp. winger. I did get a "you can't put that player in that position error" when I tried to make my right winger go a little too wide, but I'm not sure what effect that has on my RB. And I readjusted my RW back to an allowed position, of course.
I do think I have found a work-around, one that allows you to make as many adjustments mid-match as you want... at least so far.
It's easy to do, basically, just leave the default formation as your team's formation in the career mode "team management" section. However, in the pre-match screen, you can switch to whatever custom formation you want and make as many edits during the game as you please. I've experimented with this for a bit, and so far I've had no problems. I've changed player positions mid match, moved players to "illegal areas" and back, and even swapped places (usually a big no-no)... and so far, no problems in career mode.
Since with this method the career mode defaults back to the default formation after each match, I don't think it carries over any custom formation issues... hopefully eliminating any UNDEFINED player bugs.
The downsides of this formation is that you have to manually change to your custom formation each match, but this really doesn't add more than a few seconds, and since I typically make a few edits based on my opp. formation anyway, this isn't a big deal for me at all. However, it also means that you can't sim any games using anything other than the default formation, which again, for me, isn't a big deal as I don't sim games very often, and if I do, I don't really care what formation the team uses, just the result.
Anyways, I'll report back if any problems come up. Otherwise, this might be a way to safely play career mode without the UNDEFINED player bug ruining things.
Good luck, Nerf.