I'm not a fan of a beurre manie to thicken soups/sauces/gravies since it usually takes a lot more flour than I like for it to be effective. You also don't get much of a chance to cook out that raw flour taste in that environment. I read somewhere once (I can't remember the source) that a beurre manie often takes up to an hour to work properly. The only times I now use a beurre manie over a roux is if I make a last minute decision to thicken a soup/sauce/gravy or if I want extra thickening.

The only thing I can think of is that you either didn't use enough, or you didn't cook it long enough to completely thicken. Flour needs higher temperatures than other thickeners like cornstarch to fully activate.

I agree. I don't have the patience for beurre manie to thicken soups and I almost always use a roux with equal parts butter and flour. I usually add a liquid--either stock from the soup or, if it's a festive thing, cream. You can then strain the sauce and you won't have to deal with lumps.