mine has done this as well, not very often but a few times all the same, and i have let the petrol go low. The check engine light came on one time but went shortly after i filled up again.
is this what happens when you let the petrol too low?
I was guessing that the fuel filter got some crap clogged in it but freed out again after i had filled up.
EDIT: Brought my car to Jeremy in Auto Electrical Concepts to get the code read and it is:
P1410 secondary air combi valve open seized
Gonna pull it apart now to see if there is anything that I can do with it...