Where you playing as an Empire? Habitation is an Empire tech so it should only work for them. I first realized this a few beta versions back. lol I did this in a bunch of games before I finally happened to check my "completed research" list and saw that a custom tech was missing.
EDIT: I think it's just a failure to properly inform, Cerevox. And an aspect of the UI which needs refinement. The faction specific items should be greyed out when we make the selection for Kingdom or Empire. It was present during the betas so I suppose you may have that first bug report honor afterall.