Duplicate Applications Folders

When using finder to access applicatons, I found that there are 2 discrete folders which are not accesssing the same applications. If I look under my name, there is one application folder. Under the list of places seen in finder, there is another similar folder. They do not, however, always contain the same applications. In addition, when selecting certain applications from the dock, like photoshop, it states that the location has changed and asks to repair the link but does not actually repair it. The program does eventually launch. How did this happen and how do I correct it so that there is only 1 folder with all the current applications connected to the shortcuts on the dock?
Thanks in advance for any insight.