As that's likely something an inventive race will always do, I'll grant matter and energy exhaustion even though it wouldn't be in the form of 'running low on food/fuel'.
But even then, matter and energy are far more safely and easily found, harvested and retrieved if you never enter any planet's gravity well.
If you're thinking more along the lines of a hyper-space scenario, where FTL technology is achieved before self-sufficiency is solved, sure, you'd have more-traditional 'supplies' and need to land and colonize Earth-like planets.