Several things bothered me about the plotting in this episode, but the thing that bothered me most was its internal inconsistency. If Franklyn was really succeeding in exerting magical influence over his victims, then why did Nurse Rebecca Waite's magical protection fail? We are to assume that only "bad" magical systems work and "good" magical systems fail? Where's the logic in that? If I'm going to suspend logic in order to buy the premise that magic works, I need the universe I'm being asked to accept to make at least as much sense as the one I'm abandoning. Dream logic is still logic.
Neither Mulder nor Scully had much to do here--one looked up drugs in the Physician's Desk Reference and the other looked stuff up in an occult handbook. In between murders, Mulder looked at his face a lot. Especially his nose. But comic relief is supposed to relieve me from something, and there was little or no suspense here from which to be relieved.
In what is becoming a tiresome lack of respect for the character of Dana Scully, we are given no idea how she viewed or explained these strange events. She watches a team of surgeons extract scalpels teleported into a woman's stomach and all she can call it is "unexplained"? I can do that, and I didn't have to spend two years at Quantico. Scully is smarter and more capable than this. It is the backbone of the series that we are given not only Mulder's explanation for events, but some credible rationale from Scully. Leaving her slack-jawed with obtuse denial (or worse, ignorance) in the wake of wonder undermines her character.
Several things went wrong with "Sanguinarium": there was not enough material here to suspend my disbelief in magic, there was insufficient explanation of why Dr. Scully was not doing her job (examining bodies), there were too many leaps of illogic on Mulder's part (most of us would connect a ring of dots in...well, a ring). Again, the lack of fundamental cohesion in the main premise (good magic v. bad magic) worked against my acceptance of this episode on anything but the most superficial level.