I agree with
@choppadocta's definition above: a "malignant" program has an imbalance in the service (i.e., your clinical work) and educational (i.e., activities with a focus on teaching you how to be a physician) missions for residents. The description of "malignant" also often includes an implicit descriptor of the culture: program administration may minimize or completely ignore resident feedback about the program, program leadership may not support the residents within the program (which can manifest in a variety of ways), and the residents themselves may not be supportive of one another, something that may or may not be supported by a program. In typical use, though, "malignant" can mean any number of things, from true abuse of residents and completely inappropriate behavior on the part of program leadership to "I don't like what my program is doing, therefore it's malignant."
I agree with taking a description of a program as "malignant" with a grain of salt. Anyone who makes this claim should, as
@QuizzicalApe says, be able to explain why. Frankly, for many residents, residency is the first real job that they have ever had, and a lot of complaints about residency essentially boil down to being an employee for a large organization. Residency is not the same thing as college, medical school, etc., and what is expected of you is much different as an employed physician - even as a trainee - than as a student. This transition comes with some growing pains, and what some residents consider "malignant" is, instead, a reality of working in a large organization.
My residency program was quite possibly the most benign program in the world, and even then a small number of residents would complain that the program was "malignant." Perhaps not-so-coincidentally, the same residents that complained the loudest and made these claims were also often the ones that caused the most problems for the program in ways that often boiled down to simple unprofessional behavior (e.g., buying plane tickets and booking hotels to take 1+ week off on a busy inpatient service without talking to anyone about it first, then getting upset because they didn't follow clearly defined procedures for requesting and receiving vacation time - as a chief, I actually had a resident demand that the program should reimburse him/her for the flights that he/she would now no longer be able to take, lol). I would simply say that there are two sides to every complaint of a program being "malignant," and you should do your best to get as much information as you can from current/former residents, program leadership, etc. about concerns that residents might express to see what the real deal is.