No, the standard theme mobile menu links work as intended.
So turns out I was slightly wrong on my original post, the ID in the url does matter. The ID in the current url cannot be the same as the ID of the link you are trying to go to.
For example, if you are at /url1/#1 you cannot use the link /url2/#1 but you could use the link /url2/#2 or even the link /url2.
For now I have a workaround fix where I gave all the urls in my menu unique IDs, however i would like to remove this. you can reproduce the issue using inspect element and the above information.