I question the premise of “minhag overrides halacha”. There are situations in which the significance of minhag is greater than that of halacha. But overrides? For this, there needs to be a halachic opinion or precedent. This can then alter the process of reaching a conclusion to psak, being based on a particular minhag.
Let me give a few examples. One is attributed to the Chasam Sofer, and it is said that this is published (I would appreciate a citation). There was a shul in a nearby city that had a few peculiar “minhagim”. One was that when passing the center of the shul, one would bow his head. Another was that when they recited בריך שמיה prior to taking out a Sefer Torah, everyone would turn to face the back of the shul. The legend goes that the Chasam Sofer did his due diligence and discovered that the shul, prior to renovation, had had a beam on the ceiling, requiring the passer by to lower his head to not bump into it. Similarly, prior to renovation, the rear wall of the shul had a mural with the text of בריך שמיה. Since many lacked a Siddur, they would turn to face it to say that tefiloh.
Common practice does not equate with Minhag. It is quite possible that to assume that something is a minhag could be problematic. We cannot create our own minhagim. And it is possible that something becomes common practice (colloquially called minhag) but is an error. For the latter, there is a reference from a Tosafos on the first amud of Bava Basra.
So I wonder where Minhag takes precedence to Halacha.