If she has a UTI or an infection of the uterus, she'll need antibiotics.
I'd certainly have hand trimmed the area which is getting stained and 8" or so around it, but I'd have done that *before* applying the Crovect

. You can't apply more Crovect now (unless you gave less than a full dose), so it's arguably better to leave the Crovected wool in situ now.