It happens... but the GPA is a little more fuzzy than the LSAT. The lsat is standardized, thus it is a strong measure of your aptitude to succeed as a 1L in relation to the rest of the applicant pool.
The GPA, on the other hand, is a little more subjective. The GPA will be influenced by the difficulty of coursework, degree, university, grade inflation/deflation, etc. Therefore, a 3.0 physics major from Harvard is not the same as a 4.0 basket weaving major from some small unknown school that has massive grade inflation.
If you feel that your GPA is not a true indicator of your academic potential, and you have an extremely consice, strong, and legitimate argument for that, I would consider writing a GPA Addendum for schools whose GPA average is above yours.
As a final note, there was a great mock admissions panel that Kaplan recently held. On the panel were the admission deans from several top 10 law schools (harvard, u penn, nyu, etc). They evaluated 4 different fake applicants for entry into a fake law school. The applicant they selected ended up having an LSAT score just under their average and a 2.9 GPA, far from their 3.8 something average GPA. The applicant had just shined so much in every other soft factor, and had taken so many difficult courses to off set that low GPA, that they felt drawn to pick that applicant.