We are talking about a high school situation folks. Not everybody gets attention from everybody else. This disappearing act can very well have happen to many other folks as well.
Well here is what I take from this episode and how it explains your reason for finding problems.
First of all, we are on a Hellmouth. This is used to explain many an issue of the show. The mystical energy exemplifies this feeling of being 'invisible' to the point of becoming reality.
We also don't know much about this girls homelife, HOWEVER, we can assume that its not typical. She maybe an overlooked child of many, maybe her parent/s work hours that basically mean they never see her, adding to her 'no one is paying me any attention'. This is supported by the fact no one really misses her.
Even the teacher doesn't pay her attention, she is a nobody, nothing. Heck we 'see' her become invisible in a full classroom and no one says anything.
To add further to your point, you say 'We are talking about a high school situation folks. Not everybody gets attention from everybody else. This disappearing act can very well have happen to many other folks as well'.
Well if you remember how that episode ends, we 'see' that this DOES happen to others and has been a problem for a while. So you see, its not that there is a problem with the Story, just your personal understanding and acceptance mixed with your ability to think of possibilities.
We are talking about a world that has Vampires, Demons and other nasties, its not necessarily one that you can always perfectly equate to the real world.