Does it look bad to have more letters of recommendation from undergrad than masters professors in PhD admissions?
"All other things being equal," you'd rather have more references from graduate than undergraduate professors.

Your situation is such that "all other things aren't equal." Apparently, you didn't get to know any of your masters professors well, and only took one course from each. Whereas you had undergraduate professors that you took two to three courses from, and they know you better, and may be in a better position to assess your research potential.

Taking the inference a step further, you may have done your most interesting/significant research as an undergraduate, while your master's work "topped up" your academic knowledge. If that's the case, you probably ought to "go with what you've got," and get more referrals from the (undergraduate) professors that you did more work for, or at least got to know better.

I would rather have "glowing" recommendations from undergraduate professors than "lukewarm" recommendations from graduate professors.

If all else fails, try to take a second course with one of your graduate professors so the s/he can get to know you better, and give you a recommendation.