A coggins and brand inspection are not a health certificate and therefore require nothing more than visual inspection (and a blood test). If the filly did have a health certificate done, usually all that consists of is matching a horse with the coggins, quick visual, heart rate and temperature. This may have been done quickly enough that the strangles was missed, or what might be more likely is that strangles is not a reportable disease meaning that the vet might not even have to note it on the paperwork.
I checked oregon's import requirements, and they only list negative coggins, health and permit #, so the horse could easily enter with strangles.
Strangles isn't the end of the world, BUT it is an absolute responsibility that you/the barn needs to practice good management and sanitation to prevent spread and end the incubation.