Please do not punish her when she has accidents. A baby puppy is not that different than a baby human - would you punish a baby for peeing or pooping in a diaper? Of course not! Your puppy has no more bowel and bladder control than a baby does, so it's not her fault. She also does not know how to recognize when she needs to "go", so it's up to you to prevent her from doing it in the house by keeping her with you and watching her at all times, (you can actually tether her to you with a leash) or confining her in the crate when you can't take her out frequently and encourage her to go, especially before and after meals, and naps, and play.
Until she's reliably housebroken, which will probably take at least a few weeks and more likely a few months, you have to assume that she needs to potty when she's crying in her crate, unless you've just taken her out and she's already done her business. She's not going to be able to hold it for very long since she's so young. When she does potty outside, praise her enthusiastically and give her a little treat. Clean all accidents in the house with an enzyme cleaner to completely remove the smell, or it will attract her back to those spots again and again.