My Effects screen shows I have three Flame Thralls active, but I should only have one, as I just cast the spell. I don't see any other flame atronachs around when I travel or transition areas. If I summon another one, I have 4, unless I kill it, then it goes back to three.

Bug, I suppose?

Definitely a bug, I've never heard of this.

One trick to try is casting Fire Cloak. This fixes those who experience what you have except with Dead Thrall.

I can use a Bashed Patch to get up to five(possibly more?) Summoned Followers, and have had a glitched Durnheviir following My characters in the Reach as a result. This may be something to look for in Your Game? I regularly use Familiars to cancel extra Summons.

Just tried...still have two atronachs that are nowhere to be found.

Will try later, thanks.