I work with computer networks. When a system is down, I have to stay until it is running again. That might take a full 24 hours! In addition, I have to update systems after hours and on weekends (in addition to working 8-5).

One week, I had a kazillon hours built up. I didn't have a choice - I had to work it. And I was working the weekend too. I arranged with my supervisor to take half a day off on Friday so I could get some sleep. The payroll department wants to charge me half a vacation day for it. Is that right?

I personally don't think it's "right"; however, it's not illegal.

Agreed with "unfair but legal". Also, just to be clear, things like "Exempt" are a function of a federal law called FLSA. That law is interested in how people are paid based on time actually worked. That law however has little interest in hours not worked and no interest what-so-ever in what happens to things like vacation/PTO balances. Federal DOL is formally on record as saying that this is not their issue.

You mentioned "comp time". That legally does exist, but under FLSA that is solely a function of Non-Exempt employees working for the government who get comp time instead of paid overtime.

Vacation/PTO handling is strictly a function of state law and company policy. Your state is not my state, but what you describe is not normally illegal. CA is the only state that has laws anywhere that restrictive and what you describe would be legal even there.