I revived a gift certificate from my job for $300.00 when I went to use it to pay for the hotels the travel agent took his commission out of my certificate can he do that?

This one is hard to answer. Most travel agents get their commissions from the hotels, airlines etc. which just build it into what they charge you.

However, if you were responsible for paying the commission, then it didn't matter where he took it from. Also the terms of the gift certificate may be an issue.

I would ask the travel agent for a more detailed explanation also make sure you have a receipt showing the charges. If you don't get a satisfactory explanation, ask your company and the hotels.