How old is she?
It's not okay for a rabbit to have bloody urine. If your rabbit has blood in its urine, something is seriously wrong (uterine cancer, a bad infection, injury, bladder stone) and it needs to see a rabbit-savvy vet right away.
Normal rabbit urine does sometimes look reddish, and this is not a sign of blood. Rabbit urine can range in colour depending on hormones, stress levels, the foods they've eaten, how hydrated they are, the medications they're on, or even changes in the environment. Healthy rabbit urine can look clear, pale yellow, pale orange, bright reddish-orange, or bright brownish rusty red. The urine colour should vary: if it's constantly reddish, seek advice from a vet or experienced rabbit owners because a change in diet, habitat, or other aspects of care may be necessary, or something may be wrong. If your rabbit's urine is dark and smelly, that means it's dehydrated. Encourage water. If the condition continues, bring your rabbit to the vet. Dehydration can lead to GI stasis and other illnesses.
Blood in the urine will appear, if at all, in spots (often it isn't visible to the naked eye). If you're concerned, replace your rabbit's litter material with white towels, and look for red spots in the urine stains.
http://www.bio.miami.edu/hare/urinary.html
In any case, she needs to be seen by a rabbit savvy vet. Here's a list of some!
http://rabbit.org/vet-listings/
Blood clots is typically an early sign of uterine cancer OR infection. I suggest that you have an ultrasound done immediately, and then a spay if it appears to be an infection or cancer that has not spread out of the uterus.
Good luck!!
luc