This has been an issue with TX for years. And for good reason. Having a flap on a truck or trailer that is flapping wildly or runs a foot off the pavement is as good as not having no mud flap at all.
In your case it may have been a questionable stop, but there are plenty of Mexican trailers and gravel buckets running around TX with this situation and they are trying to get a handle on the problem. Just be thankful it was a warning only.