When someone says that "emotion just gets in the way", they are saying that someone's feelings and amity, their passions and sentiments, cloud their sense of practicality and force them to make a choice that seems good only because of the emotional baggage that is lost with it. If someone is ensnared in a quagmire of conflicting decisions, it is likely that they will let their emotions take control of them and make a decision based on their sentimental thought process, rather than being influenced by their completely rational thinking. Emotion, along with knowledge, is the basis of every action we take. Emotion may seem a more natural way to make actions as we are born with it. Knowledge, on the other hand, is a result of our surrounding environment and because this varies for every person, a slight problem of knowledge is created - because there will be infinite discrepancies in the varying knowledge of the different people in the world.
Most decisions are made based on one's knowledge, and because of the problem with knowledge outlined above, there is a fundamental flaw in the way we make decisions and why we consider emotion an obstacle.
Although we may be wrong in how and why we consider emotion an obstacle, there are still situations where emotion can get in the way. A good example of this is the healthcare industry. Doctors, specifically surgeons, will not agree to perform operations on their family members because they are not prepared to undergo such a daunting task with a load burdened as a result of the family ties. Even if a surgeon is the most skilled in his hospital, and will be able to do the best job, he will not perform an operation on a family member.
However, there is some good that comes out of this scenario. If the surgeon were to ignore his emotions, and do the operation anyways, he may become nervous because he is operating on a family member. In a personal sense, this could be the most important operation of his life. As a result of his nervousness, he may become jittery during the operation and make a mistake, which could have drastic consequences. So emotion, while being an obstacle, can also be a life saver.
Additionally, there are more major issues that can be influenced as a result of emotion. For example, there may be a politician who has had a relative killed as a result of a gun murder. Because of this incident, the politician may consider increased police coverage important in order to protect the citizens of the local district, even if the increased coverage results in a budget deficit. Because they were personally affected by criminal violence, they might take drastic action that may not be necessary. This is a clear situation where emotion interferes with decision making and prevents one from making the choice that is most practical or sensible.
In order to prevent emotions from getting in the way of decisions that can have severe impacts on the lives of others, measures have been taken. The best example of this is the judicial system in the United States. When random citizens are called for jury duty, it is ensured that they have no connection, whether personal or professional, to the defendant, prosecutor, or lawyers. This (to an extent) prevents jurors from making decisions based on their emotions, and instead allows them to base their verdict on the facts and evidence at hand. I say "to an extent" because jurors who know someone involved in the case in a different way, such as through business relationships, residential proximity, and the like, can simply state that they have no conflict of interest in the case and, assuming that the relationship was positive, vote in favor of the person they know. This is another problem of knowledge that arises - we will never have perfect information, so there is always a possibility of an unfair court case occurring.
These are the situations in which emotions are clear barriers in making the most sensible or right choice. When people state that "emotion just gets in the way", they are likely referring to situations where the person making the choice or decision feels strongly or is emotionally connected to the situation at hand. In these cases, accusers are justified in saying that emotion is an obstacle as it interferes with complete sensibility and prevents the making of the most practical decision.
On the other hand, there are also situations where one is affected by the emotions they feel, but does not let feelings take control of themselves. Instead, in making their decision, they make a compromise between what their sentimental and practical sides want, in effect striking a perfect balance between emotion and reason. An example is a parent who, after refusing to buy their child a toy the child wanted, is subjected to a tantrum thrown in public by the intractable child. The first reaction of the parent may be to feel utter sympathy for the child and allow them the toy, but after considering the situation thoroughly, they may decide to let the child purchase something less expensive. This balance satisfies both sides, and the parent has also been somewhat affected by emotion, which shows the humanity of the situation, but also has prevented himself from being completely taken over by the sentimental feelings, which reflects his sensibility. In addition, the child learns about how to express one's wants in a suitable fashion, so there is a lesson learned. In this case, emotion is not an obstacle - it is a drawer of compromises.
Another example of emotions influencing a person's actions is the lovestruck newlywed who splurges on his spouse without much regard as to whether or not spending the money is a wise investment. It may be a rash decision but that does not make it as emotion-based as the politician calling for more police officers in a safe neighborhood. Someone may say that emotion is interfering with reason in this scenario, but it is a little bit of a stretch. In this situation, emotion is love, and it is not an obstacle. It is simply a feeling that compels the man express his love for his wife. In this situation, one is not justified in accusing the man of allowing emotion to get in the way of reason as few people base their everyday decisions on the effect they will have a quarter century in the future.
Finally, there are situations where emotion plays absolutely no role. The example of the parent buying their child a toy can be taken to a much larger scale here - for example, buying their newly-turned-sixteen year old son a car. The son may very well want nothing but a luxury sports car. If the family is middle-class, and does not have the funds to afford a $70,000 car there is simply no question - the child either tones down his demands, or gets nothing (or gets a job). The parents in this situation are not letting their child's pleading affect their sanity. Their sensibility and practicality are trumping their emotional feeling, preventing them from making a foolish decision out of deference to their child.
In conclusion, there are many different degrees of emotion interfering with one's decision making. It can range from complete to significant to partial to absolutely none at all. The magnitude of the influence of emotion on one's choices depends on how closely one is connected with the issue at hand, the after-effects of the decision that the choice-maker considers, and, in the case of the teenager wanting the car, whether or not the situation at hand is even a question that warrants consideration. In some cases, emotion can be considered an obstacle that impairs one's judgment, but in others, it has absolutely no effect.