It's not really a blatant misuse of funds, though. My roommate is an intensely bright dude finishing up his math PhD working with studying interactions between complex systems. He writes all his code in C, and he recompiles it every time he wants to change a variable (e.g. the input file, or the number of iterations).
He's been doing it this way for years because that's what he was taught. That's the level of software engineering acumen you'll get in academia. But it "works". I've offered to help him modify the code so it will accept command line arguments, and we're going to sit down and do that so he can run several instances in parallel and utilize all of those fancypants cores on the computer I loaned him, but... he didn't know you could do that. No one told him! How would he know where to start looking that up? How reasonable is it to expect him to grok all that, when he's deep in math-land?
So it was blatant to me, software developer of four years, that something was pretty wrong, but for him: he's about to finish his PhD. He's been published a couple of times. They're not running horribly inept software development, they're running mathematics the best way they know how.