It may be a pun. Looking up magma in the French wikipedia*, another name for magma in French is groupoïde de Ore†. Here Ore is a Norwegian mathematician, but ore in English is mineral-bearing rock, whereas magma (in both English and French) is molten rock.
Would Bourbaki have based a mathematical term on this pun? I'm not in a good position to judge; maybe somebody else could comment on this.
* Since Bourbaki was a pen name used by a group of French mathematicians, this is the right language to search in.
† The other name for magma in EnglishThere is just groupoid. The additionalalso a de Ore in French suggests thatgroupoïde de Brandt, also called a groupoïdegroupoid may have had another mathematical meaning in French at the timeEnglish, which would explain why Bourbaki felt compelled to coin a new name.