The implication is that only $4000 (post tax) was spent on the game and that's an outright lie. They spent 6k on music, 5k on marketing (poster + pax), and 1k to development/demo hardware. That's not necessarily ideal but it's not entirely unreasonable either. You can argue the marketing/hardware issue perhaps, but 6k went directly into the game in the form of music.
The real lesson to take away from Star Command is their under-estimation of time and money required to create, package, and ship backer rewards. That's the real danger that other projects should be wary of.