Yeah...Don't you just LOVE IT!!!!...Get in the mission....BOOM!!!!!
If your new to the SFC Series, I can see that would be a bit of a shock...
I'm not new...And I'll tell you that this "bug" (personally, I think its a critical flaw in the game engine) has been around since SFC1 (Over 3 years) ....People here tend to call it the "Hand of Bethke".
Although it has been "addressed" in the past.....It has never been solved...Nor do I think it ever will be.
You have to remember that THIS game engine is over 3 years old...It was used in SFC1....Modified a little in SFC2 (cleaner graphics)...Modified still a little more in SFC:OP (sharper images)...And they say "totally revamped" in SFC3 (I don't see it)
The basic bugs that have been plauging the SFC series are here to stay (The one you mentioned is just one of them)