If he or she is a transgender individual, they should be use the restroom that is inline with the gender they present them-self at work.
Basically, we had a TM who was originally a 'man' and was in the 'process' of becoming a woman. Yes, we know that she was originally a guy (because she was openly transgender, but had obvious male features), but we knew her as a woman, she dressed as a woman, conducted herself as a woman.
She would use the lady's restroom, because we knew as a woman. Now, there were a couple times when she would come in as her male counterpart... When she did, she would use the male restroom.
Now, I will say, that some female TM's didn't like the fact that she would use the restroom as a "male." As such, she was asked to sit down to use the facilities.
Leave it alone. If it doesn't bother you, don't mess with it.