I am familiar with DOT regulations, and procedures (official and unofficial) for handling guide dogs and people with disabilities. Some of the comments here are "interesting," and I agree they show a lack of empathy:
1. A carrier, unless in very very specific stringent circumstances, cannot require either a person with a disability or a service animal user to provide advance notice that the person and/or a service animal will travel. Even if advance notice is provided, it would not account for flight changes due to irregular operations or other unexpected circumstances. Especially on these shuttle flights same day flight changes are common since flights run every hour.
2. There is no universal id for a service or emotion support animal, and carriers basically are required to accept the credible assurances of a passenger eg the animals master or owner. If a carrier unduly put a service animal user through the ringer, eg hassled them about their dog or disability, this could be a violation of Part 382.
3. The brass tax, and I won't sugar coat this, is that there may be circumstances when you are inconvenienced due to a carrier needing to provide a required accommodation under the Air Carrier Access Act and the accompanying 382 regulation. It sounds like you were genuinely inconvenienced by having a dog lie on your feet, but the inconvenience you suffered seems a mere nusense at best. I was inconvenienced on a BOS DCA shuttle flight yesterday as it was full, and I boarded last, and someone had put their suitcase type back in front of my seat where normally I would have leg room. This was a nusense at best, on a short flight. I could have made a federal case out of it I suppose and made them check the bag, but I grinned and beared it. I think its important for the op and others to understand their will be situations in life where you are inconvenienced and you will need to grin and bear it. If your life is so smooth and this is one of the only inconveniences you have, you are lucky. One other similar inconvenience you may have, which public may not be aware of, is that if a carrier needs a seat for an operational reason (such as accommodating a pax with a physical disability or a FAM) they can bump a passenger out of that seat even if that seat was obtained through the valid seat assignment process. Sometimes on certain carriers there is even a disclaimer when you choose your seat that it is subject to being cancelled in certain cases.
4. As noted, its best to handle this kind of situation on the spot. If you felt the dog was going to be an inconvenience that you eeither could not or wanted to choose not to deal with, I'm sure US would have put you on their next flight and waive any fees or fare differences.
5. I'm not sure how they could have handled this better. The only thing comes to mind is maybe ask for volunteers to be bumped. Sometimes agents at carriers will bump people even if its not over-sold for some sort of operational reason. This is not encouraged by company policy, but the gate agent & supervisor are the jury, judge, and governor. The agents may also have been able to ask the pax with dog if they would voluntarily take a later flight, hoepfully one in 1 hour, and maybe they could upgrade the pair as a gesture of goodwill.
6. If it came to push or shove, I would bump you instead of bumping the dog owner and dog. There is potential DOT fines & liability if you deny boarding to a passenger with a disability because that put them in a protectedc class, and it raises discrimination issues. Its a lot "easier," and less risky to just bump someone like the op who is inconvenienced. Its one thing if the op complains to the DOT they were inconvenienced and had to cool their heals in the airport bar for an hour, as opposed to a complaint that you discriminated and denied boarding to a disabled customer. Even if the op ws bumped, he hasn't documented anything here in the thread that it would be anymore than a small nusense. There could be reasons it would be more, but they are not yet listed or documented.
