What is wrong with my bike? Where is this sound coming from? My mountain bike has 3 sprockets in the front and 7 in the back. Whenever I use the center sprocket in the front there is a clicking sound. I cannot identify exactly where it is from, I don't see the chain contacting anything it shouldn't so I assume it's sections of the chain "clicking" into the sprocket teeth at certain points in the rotation. I have no idea if this is accurate, it's the only logical explanation I have at this point.

I just adjusted my front derailleurs min/max limit and shifting cable. So it should be set-up correctly. I have non issues in the lowest and highest front gear. Would anyone know why my bike makes sound while using the middle front sprocket?
If you have ruled out contact between the chain and the front derailleur, check the wear on the chainring. You may be getting 'chainsuck', where the chainring teeth hold on to the chain links as they try to peel off the bottom of the ring and carry them up until chain tension pulls them off. Often triple drivetrain bikes gets ridden in the middle ring more than the inner or outer so it makes sense this ring will wear faster than the others.

Inspect the chainring teeth, thin, pointy or sharkfin shaped teeth indicate advanced wear.   

If your chainring is worn, you probably have a worn chain and cassette also. Check the cassette sprocket teeth for signs of wear also.

The best way to check a chain is with a wear gauge, these are not very expensive. If you have to replace the cassette and one or more rings you should replace the chain as well anyway.