As the article you cited states, these injuries are ligament or bone-specific. The idea that someone can play for 10-20 years in a high contact sport with some body-wide genetic abnormality is absurd. Sure, you can get by with a weak ACL or a heart defect, but those are specific.
Murray has had issues with tendons, muscles, and bones. Further, the injuries hes has suffered would absolutely be suffered by any other player in that position. In his draft year, Murray got caught by a high hit which damaged tendons in his shoulder. This went undetected and in his draft +1 season he got hit again in the same spot and the hit separated his weakened shoulder. In a following season, Murray caught his skate in the side boards and popped his knee. It's not that he had weak knee ligaments, he just unfortunately got his skate caught. The next season, Ryan Johansen rolled up on his leg and caused a high-ankle sprain. That again would happen to anybody in Murray's situation who had Johansen fall on him.
There absolutely are players who can correctly be classified as injury-prone. Marc Savard is a prominent example given his history of numerous and recurrent concussions.
Until a specific injury pathway can be identified with Murray, we have no idea how long it will be until his next injury (if one indeed does occur) nor do we know the nature of that injury. That means he's just like most other NHL players. It's a fair bet that in any given season a player will be injured, that's the nature of the sport. But we cannot say how that injury will likely manifest.
The fact that we cannot begin to predict his next injury's timing, location, or severity means he should not be considered "injury prone."