This is an excellent question. There are many points you need to keep in mind when dealing with research and the reading of articles. Let me give you a few of these points.
First, it is important to know that all journal articles have a certain bias. They are working from a certain commonsense view of the world. For this reason, it is important to know something about the time and place each article was written. For example, if an article was written in Germany in 1910, then this was a time when rationalism was strong. This simple point can give you great insight.
Second, it is important to know the history of the scholarly literature when doing research. This is why a good place to start with any project is to see what other scholars before you have written. The first chapter of dissertations, for example, gives a brief history of scholarship. This allows you to see the trends.
Third, you should also be aware of your own cultural baggage and methods of interpretation.