While you are correct that in context the word is read Bemidbar, the name of the parsha is clearly Bamidbar. The custom has been to isolate the word or words that are the title and conjugate accordingly. This is why we have Tazriyah and not Sazriyah. Mishpatim and not HaMishpatim (since we do not use v'aileh and clarify it with asher ...). Devarim and not HaDevarim. Since the reference is to a specific desert (Sinai) the hay hayediyah is implemented. The names, according to tradition, are clearly not just the word or words of the beginning phrase.
Thursday, June 9, 2016
For some time, when I would write my Weekly Shtikle (shameless cross-promotion) for this week's פרשה, I would write it Bemidbar since that is how it is pronounced correctly. However, last year a friend of mine sent me the following convincing argument which I have accepted: