"Sorry, we do not have a bathroom."
You use 不 for every verb except for 有, where you have to use 没 for the negation. It is explained in the Tips and notes section of the Family 1 lession.
There are at least 3 other popular phrases for 'bathroom' that I believe should be accepted here:
厕所 Cè Suǒ
浴室 Yù Shì
卫生间 Wèi Shēng Jiān
The other two are correct, but I've never heard of 浴室 used in the context of a restaurant's restroom.
If you would use 一个, you would be saying "sorry, we do not have one bathroom", which would be strange in either language. Chinese doesn't have articles like a/the
有 is the only special case where you negate it with 没 instead of 不. It is explained in the Tips and notes section of the Family 1 lession.
没有 is the default negation of 有. This is ONLY the case for 有，other uses of 没 are essentially negation in the past.
I think you should have accepted 卫生间 together with 洗手间, as they are commonly used in China.