As one quick Google search will attest, Stephenie Meyer is notorious for her plot holes that could easily be explained away by magic, but which she chooses to explain with science, amateurishly. Of course, all of these "scientific" explanations come after her books publish, not in the books themselves, not that they are ever satisfying anyway. The first book in her series is not as bad as some of her later books, but it is not exempt from Meyers' plot faux pas. The following are a few of the major ones I personally spotted. Remember, these are just from the first book -- Twilight. I have left out plot holes that are later satisfactorily explained in the three subsequent books.
One of the first things that gave me pause in Twilight by Stephenie Meyer was the selective use of Bella's fainting fits brought on by blood. She faints in her biology class when they do blood typing because she can't stand the smell of blood -- yes, she can smell blood *sigh.* Earlier, she is in a car accident with a boy who winds up next to her in the hospital with "soiled" bandages on his head. There is no mention of nausea or fainting there. This selective use of Bella's weakness continues throughout the series. One can only presume that Stephenie wanted to add that Bella could smell blood and her fainting was the only way she could think of to do it, but it eventually became inconvenient.
One plot hole that I do not blame Stephenie Meyer for excluding is Bella's period -- and every other girl's period at Forks High School. Shouldn't that have had the vampires in a frenzy? Stephenie Meyer tried to explain this one away by calling menstrual blood "dead blood" or so I heard. She could have just said she found the subject distasteful, but she had to say something that makes absolutely no sense. From what I have learned of the subject, menstrual blood -- at least at the beginning of a period -- is not "dead" or "old" at all. It is just mixed with uterine tissue and eggs. It would still smell like blood to a vampire. Weak explanation is weak, Stephenie.
Speaking of blood, where the heck do the vampires store all of the blood they drink? Edward mentions he does not go to the bathroom. The only thing he mentions regurgitating is a bite of pizza. No mention is made of sweat and Myers' vampires are said to be unable to cry. I am seriously disappointed with this one. The vampires in this book should look like tick versions of Jabba the Hutt.
Okay, most people know by now that Stephenie Meyers' vampires light up like disco balls in sunlight. That is wonderful for fairy loving teens and I will not argue the silliness of that right now. What I will argue is their ability to come out in Forks because of the clouds. Mist, clouds and fog do not deter the sun's rays. You can get sunburn in a thunderstorm if it is daytime. Let us say that the UV rays are not the problem, but rather the bright light. Well, that would explain it, if the vampires did not hang out in a school cafeteria, which is presumably well lit, without any glowing effect whatsoever.
The last plot holes in the Twilight novel involve the same part of the story. There is a bit where a vampire intent on killing Bella calls her while she is at a hotel with two other vampires. The vampire that hands her the phone -- Alice -- does not notice the fact that Bella is speaking to said murderous vampire. This is odd given Stephenie Meyers' emphasis on the vampires' acute senses. Later, Bella runs away from two vampires that are protecting her to meet up with the aforementioned murderous vampire. The problem with this is that one of the vampires protecting Bella can see the future the moment someone makes a decision, but she did not stop Bella, despite presumed foreknowledge of Bella's escape.
There is no denying that Stephenie did indeed leave a lot open for scrutiny in her novels. However, these plot holes have not hurt her popularity or her wallet, so I doubt she feels the slightest twinge of regret.