Have you adopted this little one from a reputable rescue group? If so they will be happy to guide you through any issues that may arise.
How old is your puppy?
Tiolet training is very much part of owning a new puppy & requires a solid commitment for a short period of time.
I never recommend newspaper or puppy mats as it is very confusing.
As a start point you will need to thoroughly wash all bedding & any area puppy has weed on with an enzyme based cleaner. Please dont use bleach or bleach based products as it increases the scent.
This is because puppy will be attracted back to the same place he/she has already been.
Crate training over night is an option, though you will need to google this & ensure you crate train puppy properly.
Puppies need to toilet quite often, if you want this to improve, you need to address the issues & put in a solid, consistant effort. This may mean waking up during the night for a short period of time.
Take puppy outside in a safe area with some tasty treats and wait for pup to go to the toilet. You can use a verbal cue as well if you like (eg wee's)
As puppy is weeing say softly good girl, when she is finished immediately give her a treat and lots of Good Girl's!!
Take her out regularly.
Make sure you take puppy out as soon as she wakes up, straight after meals and if you notice her sniffing, circleing, or hovering around an area.
What your puppy is doing is completely natural, and is to be expected as a puppy owner. She is not unhygienic she simply hasnt been taught.
I hope this helps & good luck.
Oh, you may want to post in the puppy section as well
"There is enough love and concern for animals in every community to overcome the irresposibility of the few"