Protests in stage races are covered in Rule 4F7 in the USA Cycling Rulebook

4F7. Protest. Any protest must be submitted in writing, accompanied by a deposit as specified in the Schedule of Fees, and be filed with the race commission within the following deadlines:
(a) Concerning placings: no later than the close of sign-in for the next stage;
(b) Concerning an incident during the race: no later than one hour after the finish;
(c) Concerning the final general placings: up to 15 minutes after the official announcement;
(d) Concerning prizes owed to riders: up to one month after the official announcement.