Alright so, I was having a problem with Better Animals Plus spamming Freshwater Eels. On a hunch, I decided to test without In Control. The problem went away. The only mob rules I had that affect passive mobs, are these:

{
		"__comment": "Allow squids to spawn if there's less than 1",
		"mob": "minecraft:squid",
		"maxcount": {
			"amount": 1,
			"mob": "minecraft:squid"
		},
		"result": "default"
	},
	{
		"__comment": "Deny squids spawning if there's 1 or more",
		"mob": "minecraft:squid",
		"mincount": {
			"amount": 1,
			"mob": "minecraft:squid"
		},
		"result": "deny"
	},
	{
		"__comment": "Limit Forestry to 1 per type (mainly for butterfly spam)",
		"mod": "forestry",
		"mincount": 1,
		"result": "deny"
	},
	{
		"__comment": "Limit Exotic Birds to 1 per type for species diversity, eggs can be used to get more",
		"mod": "exoticbirds",
		"mincount": 1,
		"result": "deny"
	},
	{
		"__comment": "Limit natural passive mob spawns in general to 15 per joined player",
		"dimension": 0,
		"passive": true,
		"mincount": {
			"amount": 15,
			"passive": true,
			"perplayer": true
		},
		"result": "deny"
	}

I use some other rules for hostile mobs and didn't want to stop using In Control, so following a suggestion I tried to make a rule that would counteract whatever bug was causing the massive fish spam. I tested this:

	{
		"__comment": "Limit Better Animals Plus to 1 per type (mainly for water creature spam)",
		"mod": "betteranimalsplus",
		"mincount": 1,
		"result": "deny"
	}

And it worked. But then I noticed other mods, like Future MC, were starting to spam aquatic creatures now (Salmon). So I think there may be some kind of bug with In Control and passive aquatic spawns, affecting multiple mods. On a possibly related note, I've had a similar problem in the past with the flying lanterns in Mowzie's Mobs rapidly spawning, and I'm now wondering if it could be stemmed from the same problem.

1.12.2
incontrol-1.12-3.9.16.jar
betteranimalsplus-1.12.2-9.0.1.jar

Update: Tested Mowzie's Mobs, and the lantern spam appeared to happen with In Control present, but Mowzie says the lanterns counted as ambient mobs yet didn't increase ambient mob count, and In Control was possibly just making the spawner check the cap more often when rules are present (or something). So that's why it appeared In Control was the cause. I don't know if that's why Better Animals Plus and Future MC were spamming fish however, could be a coincidence.

Also found out that if I have no rules set, the mob spam doesn't happen with either of the 3 mods. Yet I don't have any rules that say specific passive mobs should spawn without limit. Here's my current spawn.json, including temp entries for futuremc/betteranimalsplus/mowzies to stop the spam:
spawn.txt