One easy fix for the non-career to career skill bug would be to give yourself an extra 5 XP (that should be what it costs to get the level 1 skill once it is a career skill). It may not be the prettiest or best solution, but it would work. Or maybe you don't restrict the human skills they can choose based on their career/specialization?
Yeah, the extra XP is a work-around, but then you as both player and GM need to remember where that extra XP came from in the first place, so it's not exactly an elegant solution.
As for the not restricting the Human bonus skills, that's a possibility, particularly since most players are probably going to remember what their career skills are from their initial career & spec anyway.