As a Fate GM, you shouldn't be nickel-and-diming Advantages in conflicts.
There are actually three separate vectors here that have all plotted a collision course with your game to make it less exciting than it could be, so let's take them out one at a time.
Are You Too Conflicted?
There's some advice in Fate Core that honestly goes a little too far:
If someone tries to attack in a contest, then they're doing direct harm, and it ceases to be a contest. You should immediately stop what you're doing and start setting up for a conflict instead.
-- "Attacks in a Contest", from the SRD
But that's not entirely true. "As long as the characters involved have both the intent and the ability to harm one another, then you're in a conflict scene." ("Conflicts", from the SRD, emphasis mine) If you're trying to get away from someone who wants to hurt you -- you don't intend to hurt them -- then you're not in a conflict scene. You're in... some kind of contest/conflict hybrid.
It sounds like the scene you're describing falls in that weird middle part. The PCs want out of the temple, your NPCs want to capture them -- even if this has reached the point where your NPCs have cornered or outnumbered the PCs to the point that they can force attacks on them, it doesn't have to operate as a full conflict if your PCs would rather escape than fight, or if the total number of NPCs you could bring to bear make an actual fight a very unlikely victory.
The first time I remember seeing this floated was in Dresden Files Accelerated, which interspersed contest and conflict rounds for people who were trying to accomplish something else while a conflict was going on, and it's undergone some more development since then until landing in Fate Condensed:
In a contest, the PCs can't or aren't trying to harm the enemy. External threats (e.g., erupting volcano, angry god) may attack any or all sides; those threats might also be a participant in the contest.
-- "Contests", from the Condensed SRD
In that case, create an advantage risks your turn as usual, and your contest roll is also your defense roll. Every PC should be making their own contest roll unless they'd be depending on one PC to defend them, like the driver of their getaway chariot or whatever.
When two sides are trying to accomplish different things and they aren't both willing and able to harm each other to do it, you shouldn't run it as a conflict in the first place. And again, that's "harm" as in "total narrative control". Sometimes you do want to knock out all the guards so you can do an extended search of a warehouse (for example), but consider a smaller case, where you're trying to leave a warehouse in a hurry and there are a couple guards blocking the most obvious door.
Sure, the way that it plays out is that Twilliam distracts the guards, Athens follows up on that from a blind angle to knock them clear of the door, and then Starhound shoots the lock out and you're gone, but you don't need to get total control of the guards to pull that off, just get them out of the way for a second - this can just as easily be run as a challenge as a conflict.
By limiting conflicts to the times when one side needs to control another, rather than just the times when one side is opposing another, you'll only be spinning up conflicts when you need to, reducing the often-repetitive nature of small conflicts.
Small conflicts shouldn't use Advantages for numbers, and casual conflicts should be small
By "small" I mean "mostly involving mooks or nameless NPCs". Maybe a supporting NPC but that's as high as it goes. In those cases, maybe the supporting NPC is there to actually provide some kind of narrative, but what you're after is more the texture of conflict - your opposition has every intention of winning, but from a dramatic standpoint this isn't a battle the heroes have much chance of losing.
Again, keep in mind - this is a case where you have to control your opposition to get what you want. Sometimes it happens, with varying frequency depending on what genre you're running, but just because it's happening doesn't necessarily mean it's a big dramatic production that needs a bunch of supporting or main NPCs made for it.
In those cases, you don't go after numbers by individually having your NPCs try to create Advantages or counter PC advantages. You go for numbers by having your NPCs coordinate attacks to stack up a teamwork bonus, and by spending Fate Points from the scene pool. When you're starting to run low on nameless NPCs and the scene pool is empty it's probably time to concede out of the fight rather than running it to the bitter end.
In the big conflicts, your Advantages should be spectacular
When facing down roughly equal numbers of supporting NPCs, or a main NPC, you're in a conflict that the story turns on, and you should go big with your own Advantages, to the point of, well:
Invariably, if you play Fate long enough, someone's going to try to affect multiple people at once in a conflict.
The easiest way to do this is to create an advantage on the scene, rather than on a specific target. A Gas-Filled Room has the potential to affect everyone in it, and it's not too much of a stretch to suggest that the Inspirational Mood in a room could be contagious. In this context, the aspect presents an excuse to call for a skill roll (using the overcome action) from anyone in the scene who attempts to get past it. Generally speaking, it won't cause damage, but it will make things more difficult for those affected.
Likewise, keep in mind that your NPCs have a home turf advantage in conflicts if the PCs go to them in order to resolve something. So, when you’re setting up situation aspects, you can pre-load the NPC with some free invocations if it’s reasonable that they’ve had time to place those aspects.
and, well, Advantages are Aspects and Aspects are true... until they're not. A scene or zone or personal aspect created by your NPCs, possibly when using their prep, could just cancel out PC advantages. Your main NPC's been dogpiled and restrained? Now they've got a Sparking Golden Force Field and none of that matters because nobody can lay a hand on them. PCs are hiding and taking aim? Now the whole place is Flooded With Black-Hole Light and none of that works anymore. PCs have created cover or obstacles? Now their adversaries have the Flight of the False Gods.
If NPCs in the big showstopper fights can just slam down an Advantage and clear the board (again, because this is a showstopper fight and your NPCs have prepared for this) then that takes round-to-round Advantage shepherding completely off the table for your PCs - they'll need to deal with these big impactful Advantages from you, and do what they can with their personally-created Advantages while they have them.
And one final note:
Your players might be playing too defensively.
Mentioning that your players spend their free invokes on defense reminded me of a common antipattern I saw running Fate demos that a more experienced GM was kind enough to caution me against. Fate Points and free invokes are there to help you the player make cool things happen. When you spend them on defense, what you're doing instead is making nothing happen, and "nothing" isn't cool.
You're not forbidden from spending them on defense because doing it might stop you from getting Taken Out, and "never anything again" is even less cool than "nothing", but by and large you should spend your stress bar on defense, since that's what it's there for, and spend Fate Points and free invokes on making cool things happen. Otherwise you'll just be making nothing happen, and your situation sounds like there's a lot more nothing happening than anyone wants.
There may be something similar you're familiar with if you're coming to Fate from Pathfinder, or 3rd or 5th edition D&D: don't use magic to heal in combat. Sure, you can spend your turn and those resources to partly roll back the damage the other side did on their turn, and sometimes the benefit is big enough to warrant it, like bringing somebody else back into the fight. But most of the time, you're better off spending those resources to help your side win faster instead of losing slower.
Fate Points and free invokes work the same way.