Her crate used as her sleeping area should never be used as part of a reprimand, it is confusing for the puppy. You can try placing her in a small unfamiliar room like a closet or laundry. The most important feeling for her is your acceptance and interaction with her so the idea behind "time out" is for her to feel that this in in jeopardy. Some puppies respond to the "time out" because they are anxious about the situation, others just take it in stride and take a nap. If standard approaches to "time out" are not working you can try putting her on a short leash and fixing it to say a heavy chair leg so that she can see you or the family but not participate. Other measures are using noise like a can full of coins or some people have success with a bicycle horn or even a small air horn. Try to think of something she does not like and build it into the corrective measure. Some examples that owners have shared are the vacuum cleaner or a hair dryer.
Many times it can help if you let me know what you are doing now, also trying to bring about the desired response is tougher now that you have had her several weeks. You pretty much have to start over.
This means for the next week or two your puppy should be in her crate, door closed if she is not actively engaged with your family. After this initial period you can go to using a small room (bathroom) or an attached play pen with the door left open. Many people try to go from the confined space of the cage to free run of the house and usually get frustrated with the accidents. Your puppy has to learn what you expect and how to comply. As she approaches 12-14 weeks of age and control over elimination is improving then free run can work.