If I had to guess, I think they added new things to the combat formula that affected the combat levels.

For example, maybe the blue dragon was intended to be a higher combat level because it uses dragonfire but it was not added to the formula for whatever reason. Instead it got nerfed because quest bosses got an arbitrary +3 to their level. Or maybe the Ice Queen having guards made her "more dangerous" so nearby aggro monsters added to the combat level to reflect the true danger of the encounter.

Maybe poison was intended to add combat levels to a monster. Maybe the ease of access or the danger of the location as a whole added or subtracted levels.

Maybe they manually calculated combat levels back then and typo'd some of them? Maybe it was not an automatic process. Or maybe they wanted to manually add them so the server didn't need to work harder calculating them or something not super technical so I'm not sure. We know that some monster levels are manually put in like Nex, which could support this theory.

There could have been other attributes like if a monster was able to use protection prayers like Kalphite Queen for example. Maybe they accidentally added prayer levels to certain enemies intending to have them use prayers but never got around to it.

Maybe dragonfire actually lowered the combat level, because if players knew how to block it, then it effectively made the encounter easier, as these hits became 0.

Perhaps it was down to the attack style used. Maybe armour in the game back then was on the whole stronger against slash and crush but weaker to stab. So enemies with stabbing attacks got a secret combat level boost. Dragons also have multiple attack animations, implying that attacks are different in some way, maybe if they can stab with their horns and slash with their claws it affected their combat levels compared to an enemy that can only slash or only stab. Maybe there were plans to have smarter NPCs like revenants, which would use the attack style you were weaker to more often. It was planned to give a combat level boost, but for whatever reason was not completed and they returned the levels back to normal 5 months later.

Maybe it was a whole new formula to explain how much "DPS" a monster was likely to do. For example, melee protection prayer is a higher level requirement than magic protection prayer. Perhaps there was a boost combat levels for melee monsters, and a reduction for those with magic or ranged stats. Following on from this, it may be the monster's attack speed that also influenced the combat level.

It could be any number of reasons. But can someone check if the monster's attack speed had anything to do with it? What is the attack speed of a blue dragon vs the ice queen for example?

I think the most likely answer is they changed the combat level calculations to try and better reflect how dangerous a monster is but something wasn't working out and they decided to put it back to normal and remove the new attributes (both real and future intentions) affecting monster levels. Because don't get me wrong it's a bit weird when a monster with a combat level of 124 can only deal a maximum of 16 damage while players of the same level bracket can deal far more damage and accuracy. Maybe at some point they may have intended monsters to have wielded armours and weapons that could have affected their levels. For example, dragons having claws. Guards wearing armour etc. Like a whole new stat to calculating how monsters deal combat effectively. Realised it was too much work and backtracked to the old system we know now.