Yes, they had clearly not trained for realistic infantry types of situations or even real fighting types of situations. There are most certainly bad habits that people can get into by becoming too comfortable within sporting rules sets.
In their defense though, there aren't too many schools/instructors out there who teach skill sets (like boxing, wrestling, BJJ) at a very high level who also truly understand and teach the differences between sport combat and real combat. Many times the students must come to these realizations on their own (either through experiences like in the video, real fights they've been in, etc...) or be lucky enough/smart enough to find someone who does understand the differences.
Like you said though, they probably would have whooped on most if not all of those Marines inside an MMA cage/ring. It's a matter of specificity of training, not that they are necessarily learning different skills (for instance both learn how to effectively strike, takedowns, submissions/breaks, and defenses to all of the above), even though there is some of that too (the Marines train to use weapons for example which MMA fighters do not).