I got a B+ in a seminar in my PhD program last spring. I'd never received anything below an A in my field before then, and seriously considered completely dropping out of the program because I'd never heard of another student in the program getting a course grade lower than an A-. This year, I consulted with a professor I trust about it, and he told me first that he received a B+ in a seminar his first year of graduate school, and then that B grades here were far more common than I thought (that at least 5 or so of them were given each quarter amongst the 20-ish students taking courses in the department).
To offer further confirmation that a B in a graduate course isn't a mark of doom, I sent out transfer applications to other universities this year, and was awarded a university-wide fellowship at a very large R1 university with just a bit under 10,000 masters and doctoral students. You don't want like 10 Bs, but I don't think for a second that 1 or 2 is going to make any difference at all. In fact, having marks below an A might indicate that your program's grades aren't so inflated that they don't mean anything.