I am not sure if they will let you file this far after the event but you might try filing FMLA paperwork.
Granted it only protects your job twelve weeks but she would still be under the protected time. Definitely you need to talk to HR.
For future reference, get everything in writing and be sure to file FMLA when needed.
I don't know if you know this but because this was a case where she was on STD you might have been able to file yourself as primary care taker if you needed to take time off to take her to the doctor or things of that nature.
They normally require 30 days notice before taking time off in large chunks but FMLA can be used for single days as well.