I just got a new maltezer pup after my best friend of 14 years (which is pretty damn good for a dog, even a small one) passed away, she was also a maltezer and the greatest dog of all time.

The new pup can run around freely all day but at night I want her to sleep in her bench because she still pees inside from time to time (3 months old now).

I just put her inside her bench for the night but she's crying and it's breaking my heart. Please tell me if I'm right to do so and if not what can I do better?

pic related is a blurry pic of her due to flash (didn't want to wake her with it)