First question - how did you find this out? Did a school staff person tell you, your ds, someone else? I'm just curious about the situation that caused it to come to light.
Re following up, regardless of where specific records are kept within the district, you can document this by sending an email to every member of your ds' IEP team, quoting the accommodation directly from the IEP, state the date the accommodation went into the IEP, state the tests that have been given since without accommodation, state that you expect the IEP accommodations to be followed. You can end by giving the school staff the opportunity to reply if there is something you've stated that is not what they understand the situation to be (i.e. give them a chance to respond if they feel your information is incorrect).
By writing this out and sending it in via email you've created documentation. If the school wants to refute what you've said, they can do that by responding.
Re the scores being on your ds' school record - is he in elementary school? If so, I'd try not to worry too much over it. Absolutely document this and request a flag be added to those test scores, but if nothing happens retroactively don't get caught up in worry over it. For the most part (other than possibly academic group tracking) elementary school scores don't matter once your child has moved on and up in school. Instead just keep focused on making sure accommodations are followed from this point forward. If there is a score that's prevented him access to some type of program because it was too low, then I'd request (in writing) that he be retested for admission to the program, with accommodations in place.
Even if there is no "flag" added to your ds' test records, be sure to keep your own list of which tests did not include accommodations, so you'll have the data for any future discussions you're involved with the school in which test results are discussed or used as data.
We had difficulty with our school following accommodations - and although I don't know that this will happen with your school, the thing that was the biggest issue for us ultimately (aside from the simple fact that ds didn't receive his accommodations) - was that the school tried to use his *not* using them as reason to take the accommodations away. Even though it wasn't ds' choice not to use them (picture me banging my head repeatedly into a big brick wall over this!)..... I hope the same doesn't happen at your school!
Best wishes,
polarbear
ps - I wonder if you need to request that there be more specific wording added to the IEP for "alternate assessment"? I'm not familiar with what that would be, and I know that it's best to not be too specific on an IEP in order to not make an accommodation so specific it becomes impossible to accomplish (for instance, my ds had an accommodation for use of a word processor, but we were cautioned not to specifically say "iPad" or "computer" etc because he might be in a situation where one or the other wasn't available - hope that makes sense). Do you have a local parent advocate group (either school advocate group or disability law group) that offers advice at no charge? If you have access to such a group, I'd ask about what they recommend for the specific words used in the IEP. You can also ask them if it's possible to flag tests already given to show that accommodations weren't provided.
