The abominations spawn out of a particular tree stump. Get too close to it, and the abominations grow. (I've played with it with the BetterCreative mod to see how it appears.) So you might have cleared the area but eventually ran too close to one of those stumps while avoiding BM.

So it's a little bad luck and a little being ill-prepared. There's various ways you can tackle that situation. It's easy enough to kite the abomination away, jump up onto a tree where neither can get you and shoot the thing dead, or you can use an axe/spear and shield combo and take it out in about 10 seconds - he's easy to block and stagger. Getting up high can also assist with solo-ing BM but the best mace you can manage and frost arrows do superb damage on him and the minions he summons.

The /killall command kills EVERYTHING so... no, that's not really a fair fight. ;)