That looks like a bug. I would report it to Wolfram Support. One workaround would be to remove trailing hyphens.
sentence = "through the mechanism of follow-up of living patients
the natural history of various diseases of military-medical
importance";
sentence // TextWords // DeleteStopwords // StringReplace["-" ~~ EndOfString -> ""]
(* {"mechanism", "follow", "living", "patients", "natural", "history", "various", "diseases", "military-medical", "importance"} *)