No seat assignment is actually ever guaranteed unfortunately. However in your case it sounds like a travel agent issue. I have found problems with seat assignments is not uncommon when using a 3rd party (i.e. travel agents or even another airline). Usually when requesting a seat assignment via a 3rd party, its just that, a request. That request can either be accepted, denied or sometimes never even received. Also possibly, many times travel agents/3rd parties will show all available seat assignments on a seat map (even including seats you arent necessarily entitled to like preferred or choice seats). Their systems will let you select these seats when you really shouldn't be able to. So going back to the seat request concept, when you select one of these seats via the 3rd party that you aren't entitled to, the US system rejects the request or you end up in a situation where you have to pay for the seat assignment since the seat picked is a choice seat. US has a program in which some seat assignments in coach are considered choice seats which come with a fee.

I've encountered problems like this time and time again when using a 3rd party to book airline travel as I do most of the time when at least traveling for work. So this problem most likely is not a US problem but a problem with the travel agent you used. I'd go back to them with the complaint.