The mouse will work fine for the most part on the top and side bar but as soon as I open up anything the mouse won't click on anything. I can still move the move around, but cannot click on anything. I've been searching for a solution but it seems like a lot of people have this problem but also seems like there is no solution. Anyone?
Any hardware info is required; it could be that your RAM-memory is too low and Ubuntu has difficulty to settle. This comes alive when you open apps from the side bar. Keep in mind that Unity actually needs, for a good work-flow, for about 1.5 Gb of RAM-memory (my own standards). Seems to me that is the problem with your machine.
Of course, trying a different mouse could learn you if your mouse is bad (or the connector is bad).
Anyhow please let us know what your computer is made of (RAM / CPU / Graphic card)