Welcome to the forum.
First things first - is she peeing more than usual during the day as well as during the night? She may have a slight urinary infection, which is making it more difficult for her to exercise bladder control. Or, if she is not already spayed, she could be coming into heat, which often causes bitches to need to go more often.
As you say this has happened several times, I think you may have confused her by teaching her to toilet in the crate - does she also sleep there? Does it have soft, absorbant material in it? Material that to a dog feels very much like your bed?
House training makes use of a dog's natural instinct not to soil the area where it sleeps - crates are usually used as a sleeping area, so that the puppy avoids toiletting there. Once she is old enough to have some control, she is taught that the whole house is "den", to be kept clean. If a dog once learns to pee and poo where she sleeps you have a bigger job on your hands to retrain her.
If the crate is set up as a dog toilet, rather than with soft materials, does she have easy access to it at night, when she is sleeping with you? If she has been used to being able to reiieve herself during the night, she may find it very difficult to last till morning. Either make her a bed where she can get to her toilet area, set up a toilet area near your bed and make sure she knows how to use it, or train yourself to wake up and take her out every few hours! If you set an alarm, you can slowly increase the time you sleep until she can cope with all night.
Don't make a fuss if you find a mess - and if you catch her in the act a do a quick interrupt, lift her onto the toilet place, and treat and praise her for doing it in the right place. Toilet training is all about ensuring the dog has the minimum opportunities for getting it wrong - which is why teaching them to go outside, where it is so obviously different, is usually easier than teaching them the difference between permitted/not permitted areas in the house! But many people have successfully taught their dogs to use an indoor toilet - the key seems to be to make it as different from carpeting, bedding and other soft furnishings and floor coverings as possible.
Finally, you will need to use an enzyme cleaner or biological washing powder on your bedding to remove all the smell, or the scent of urine will continue to encourage her to use that spot. Don't get too discouraged - she is still a puppy, and with calm, kind management and training you will both get this sorted.
To sit with a dog on a hillside on a glorious afternoon is to be back in Eden,
where doing nothing was not boring- it was peace.
~ Milan Kundera