New Subaru pops out of gear

My wife and I purchased a new 2009 Subaru Outback in December of 2008. It currently has about 5000 miles. It has a manual 5-speed transmission.

When in stop and go traffic, if I am in first or second gear and not accelerating, the car pretty regularly pops out of gear. I have driven a standard transmission for aobut 20 years, and have never had this problem on other vehicles (which were all pre 1995 models). I am concerned that there is something wrong with this car’s transmission and that this seemingly minor problem will develop into something worse once the warranty is gone. This isn’t standard behavior is it?

No. Take it back to the dealer as a warranty complaint. Let them investigate and respond to your complaint. Make sure all that is said is in writing.

This is not normal.

Has it done this since Day One or is something that has recently cropped up?
Do you do a lot of city stop and go driving?
There’s a reason for the questions.

This is likely an internal problem and is warrantable, meaning that it should be a free fix to you.
The questions are simply to determine if this was a factory assembly error or possibly exacerbated by your driving habits or a combination of both.

(Don’t read anything into my comment about your driving habits please.)

This is not normal for any new car, and why the OP would tolerate it is something that I don’t understand. Just as with any other significant problem on a new car, it should be taken back to the dealership a.s.a.p. for examination of the transmission and for free repair. Keep all documentation just in case you need to press your case under the Lemon Law in your state.