All the time. Negative thoughts are normal and increase as you learn more and can see where the flaws in your work are. The more you learn, the worse it gets, until at some point you'll be confident enough to look at your work and defend your choices (to you and to others).

This doesn't really have much to do with working alone, but it is harder to grow if you can't get feedback and aren't forced to explain your code to others.

If (like me) you are physically unable to get together with your peers IRL to discuss your work (for instance, because you're about 1000km away from the nearest person you can conceivable discuss things with), you should find other ways to do this. IRC is good, putting code up in github for feedback, blogging about it, these all help kickstart the next round of learning.

You may feel worse about your code once you get some external eyeballs on it, but it's likely you'll get positive feedback, which is always comforting.

There's no aboiding negative thoughts, it's a sign that you are striving to do better. Start worrying when you don't think you can do better.