I don't like going to my girlfriend's house
Why don't you like going to your girlfriend's house?
I feel uncomfortable. Her house is too messy.
Messy houses are dirty, but that shouldn't stop you from visiting her to show your true love for her. Otherwise, she might think you are just using her for sexual purposes.
I love her, but have issues with the condition of her house.
If you  feel uncomfortable, then it's time to have a polite, respectful conversation with her. Maybe you could offer to help her keep the house more tidy.