Someone told me that it is not always a good idea to defragment a minimally fragmented drive (<2%); and that it could cause performance issues.
Are they right, and why/why not?
No, if you want to spend the time doing that it's fine. Generally you won't get much for the time you spend doing it, though.
Keep in mind that the 2% metric, however, doesn't tell you anything. Does that mean that only 2% of files are fragmented, or that 2% of the drive space has file fragments, or something else?
For certain metrics a 2% fragmented drive might actually be slowing you down significantly depending on your usage pattern.
Still, in most cases the time it takes to defragment it is vastly longer than the time you'll save once it's defragmented.
As Adam said, the only performance issue caused by defragging an almost-unfragmented drive is the time it takes to run the defrag. But note that the less fragmented a drive is, the quicker the defrag will run.