This doesn't often happen in any sort of series or film and I am surprised that it would occur in a series that was as popular as this one and one that likely had a tremendous amount of resources associated with it.
Normally, when you are dealing with films or series that have a budget that's worth talking about, they have a team of people whose job is only to ensure that the various scenes have proper flow and things are not out of place in a way that makes sense. I have worked on several low-budget films and there are people whose only job is to review footage before another take is done and they will single out things with such minute detail such as how much beverage was left in a person's glass and whether or not the drink was in the person's hand or not when angles were changed. It is quite rare that this ever gets violated but I have noticed this in several instances of just Scrubs as well as many others.
These people who have this job are also in charge of making sure that something that doesn't belong wherever the show is meant to be taking place isn't in the scenes.
You may recall the rather famous screw up as far as this is concerned in an episode of Game of Thrones where a modern coffee cup was on the table in a scene. This happened more than once in that series and I am certain someone got seriously chewed out for that one and it probably wasn't Emilia Clark either even though it was ultimately her fault.
In Scrubs, the viewership started to seriously wane around season 6 and perhaps the staff were a bit burned out and things started to slip a bit as far as how much they cared during production. They had gone from rank 14 in the overall ratings to rank 87 at this point and they were teetering on the brink of whether or not it had enough viewers for NBC to stay interested in it. Shortly after season 6 they dropped to 114 and were sold to ABC. There might have been internal squabbles that lead to this rather HUGE problem in continuity happening because it had to have been noticed by a large portion of the cast and crew but apparently they just didn't care. It is episode 11 and entitled "My Night to Remember."
Dr. Cox, one of the central and some would argue the "best" character, turns up in the middle of the episode with a shaved head. There is no lead in to this happening and as far as I know nobody even mentions it, even though this is a dramatic new look for the doc that definitely would have been discussed. I actually started to question if I had missed something and went back and episode to see if I had. But I was correct, there was a problem here. In the previous episode he had a head of hair at the end of it and in this episode (which seemed to be a lazy sort of filler episode anyway) he just turns up looking like this with no reaction from fellow cast members.
In the very next episode entitled "My Fishbowl" I was stunned to discover that Dr. Cox walks in and now has a full head of hair again.
He continues to have this full head of hair through what was likely considered the "flagship" episodes of the season where one of the main characters that has been there from the start gets killed off. It is a tear-jerker and a really good duo of episodes were Laverne is in a coma and everyone has to say goodbye to her in episodes 14 and 15. Dr. Cox was a central character in this because just the day before she goes into her coma, he and Laverne had a rather heated discussion about the existence of God.
After Laverne dies and her funeral happens that is the point where Dr. Cox decides to shave his head in the timeline of the show.
It is at this point that the other characters start to poke fun at him for this choice and of course JD admires it and fantasizes about he also having a shaved head.
This is a major continuity mistake and one that the producers would later admit that they were aware of it but by the time they had lined up all the episodes it would have taken too much time and money to re-shoot all the scenes involved. You see, as you might expect the episodes are not shot in a linear fashion. Often, when the actors would turn up for work, they didn't actually know where they were in terms of the flow of the season. As far as John C. McGinley (Dr. Cox) was concerned, he was doing what he was told and these decisions were not up to him. There isn't much talk among the actors about noticing the mistake because they didn't concern themselves with such things when shooting.
I recall from my own experience working on films that the director and producers treat the shooting as a "need to know" sort of thing. On one particular film I was on we shot the ending scenes of a low-budget horror movie on the first days of production and even though I was not one of the "need to know people" I prodded the Assistant Director who I had befriended at the bar early on and he informed me that they were unsure about their budget and these scenes were the most expensive ones and they absolutely needed those scenes for the film to work. Then, later, they would film the rest of the movie with whatever money was left over.
This wasn't the case with Scrubs though. What happened here was a big screw up but by the time they figured it out it was too late to do anything about it. The hopes with one of the producers was that this slip up would make the news and then people who were not watching already would tune back in. Well, it might have worked a bit because episodes 16 and 17 (immediately following the episode where Dr. Cox shaved his head, there was a slight bump in the viewership and then it crashed back down.
I think Scrubs is a fantastic show and this is my 4th or 5th rewatch of it. I feel as though season 6 started looking like the "beginning of the end" because not only was this huge mistake in the final cut, but the episodes generally speaking started to feel less polished as a whole. The stories were losing steam and the writing simply wasn't as good as it had been in all 5 of the previous seasons. I suppose it perhaps wasn't a coincidence that in the following season, they would lose their contract with NBC and travel over to ABC.