It's not common, but it happens... a team is given back their timeout if subsequent rulings on the field negate the reason for the timeout being called. In this case, the ruling on the field was the play was stopped short of the line to gain, so the clock would keep running. BSU called a timeout to stop the clock. Subsequent rulings (the measurement and resulting call of first down) negated the reason for the original timeout, so it was correctly, by rule, restored to them. They used it to challenge the spot. They won the challenge, so the timeout was correctly, by rule, restored to them. Then they used the timeout again because the original conditions that resulted in them using the timeout in the first place had been restored (4th down, clock to be restarted).