Genjutsu Detection:
In essence there are two ways to detect genjutsu: either figure out its an illusion or notice the fluctuation on your chakra flow. To figure out its an illusion, the target needs to analyze the information he is receiving from the illusion and detect what is wrong with it or performing an educated guess. While the most used method, its also the most flawed and, regardless of any fact, is nothing more than a gamble as ones reasoning can always be wrong. Its also sometimes slow, as some illusions are very detailed and perfected to the point that noticing its an illusion may be virtually impossible. Detecting the fluctuation in your chakra flow depends on the situation but mainly depends on your abilities as only Doujutsu or Sensory Ninjas can have ways to detect fluctuations in ones chakra flow. Doujutsu users have, however, a limitation that hinders them to a bigger degree: if the illusion is high ranked (A-Rank for Byakugan and Rinnegan, while on the Sharingan, dependent on its stage) and takes complete control over their eyesight, they can't see their own chakra flow as what they will see is what is the illusion. Chakra sensors on the other hand need to figure out its a genjutsu or that something is wrong to then will themselves to focus on their chakra flow and notice its fluctuation unless they have the Chakra Sensing technique already active. Basically, if they don't figure out nothing is wrong, they won't sense themselves. This means that Chakra Sensoring ninjas work on a hybrid basis. In one hand they need to figure out some minor sign that its an illusion but on the other hand once its found they can use their sensing abilities to confirm it without a doubt.
One misconception generally associated with Genjutsu is that ones chakra travells to ones target. This is false or, if true, was never proven or showed in the manga/anime. If this was the case, we would never see Doujutsu or Chakra Sensory users getting caught in Genjutsu as they "would see it coming".
Another point that leads to many discussions is the fact that Clones may or may not be affected by Illusions. The truth is that they are in fact affected by illusions but since they don't have an organic, real body, they don't suffer pain or reflexive actions based on that illusion. They will experience it and see it and be affected by it in terms of their senses, but they don't take mental or otherwise physical damage nor do they experience suffering or torture, faint or otherwise fall asleep or become paralyzed as a result of the Illusion.