we are doing the whole Falcon's Hollow series if anyone is familiar.

I love that series! For anyone that doesn't know, it uses 2 free modules and 2 or 3 paid modules from Paizo -- all are set in the town of Falcon's Hollow. If you get all the modules ahead of time, you can tally up the NPCs and populate the town really well, lots of interesting personalities, low-level shops, etc. Also good for beginner GMs because there is no such thing as a big town or magic shop. So the only magic you have to contend with is (mostly) what's in the modules. The series is Hollow's Last Hope -> Crown of the Kobold King -> Revenge of the Kobold King -> Hungry are the Dead. And then you can throw in Carnival of Tears before or after Hungry are the Dead, if you are up for a really disturbing game.

When we start back up one of the players could no longer play so we were stuck with 3 people.

OK. Pathfinder's system assumes 4 or 5 PCs are a normal team. Having 3 would normally be a problem... however, in this situation you are posting into the Pathfinder forum, yet the modules are for D&D 3.5 edition. That's not a problem, that means your solution is at hand. If you run 3 Pathfinder characters through a Pathfinder module, they will be underpowered. They will need to run away often, and might die. But this is, if I understand correctly, a bunch of Pathfinder characters using Pathfinder rules, but going through a D&D 3.5 module. 3.5 is wimpy compared to Pathfinder, so your team of 3 should be fine! Adjust (almost) nothing!

the party happened to fall upon a Manticore.

Here is the D&D 3.5 manticore. As you can see, it should murder an entire 2nd level party, even if there are 6 or 7 of them. It can fly, gets 6 ranged attacks per round, and can do flyby attacks. Your 2nd level party probably cannot get into the air. And a manticore is many times smarter than an animal. It should never land and go toe-to-toe with adventurers. So if you run this fairly, all PCs should be dead.

Why did the module authors add this encounter?!?! Well, let's address 2 things about it.

1. Tons of modules that are sandboxy or contain wandering monster charts will have an overpowering encounter or two, simply to simulate game world reality. That is, the world isn't level-balanced. There are powerful enemies that need powerful heroes, and when the PCs are not yet powerful enough, they shouldn't be acting like big damn heroes. It's a lesson in running, and it keeps the game elevated with a correct amount of tension: the players will never know if the encounters are OK for them, so they will never shrug and say, "It has to be safe, so kill everything and everyone." It helps curb murderhobo behavior, and that's a good thing. For example, later on, the PCs might confront the leaders of the lumber consortium in Falcon's Hollow. Those guys are tough. They have -- I am not kidding -- about 200 armed mercenaries at their beck & call. If the players think "charge in, let's take them all out" they are INSANE. But you need establishing fights like the manticore to help frame the context of the game world: it's dangerous and some fights might be unwise.
2. The module author himself addresses this issue on page 8. He writes, "Some of these encounters are extremely dangerous." And later, "Don't hesitate to fudge a little and supply them with a different result. Also the manner in which you narrate the beginning of the encounter should allow the PCs a chance to deal with it in more ways than just hurtling into combat." He goes on to mention that there is also a hill giant encounter, which might be talked through, if the PCs are careful.

Let's look at that 2nd point. The wandering monster listing says that the manticore encounter starts with them finding a dire wolf corpse that has a bunch of manticore spikes sticking out of its body. Even if they cannot make the skill check to determine what did it, they should now have a hint that something powerful enough to prey on dire wolves is nearby. When the manticore appears, they should know to run or at least be extremely cautious. They should not engage it directly. They should snipe at it from the trees or other terrain that gives them some advantage and/or escape. If they don't, that's their fault (assuming you are a fair GM and give them some terrain to use). Also, when the manticore appears, they should be able to take a knowledge (arcana) check to determine if they know what the creature is. You can even suggest it. If you do the standard Pathfinder handling of monster checks, then a DC of 16 would let them know basics (a lion with dragon wings & spiked tail, able to fling many spikes per round, vaguely "more powerful than a dire wolf"). A DC of 21 would allow them to ask 1 question, maybe "what does the stat line for hit points look like?" Then you could tell them it has 57 hit points and 6 hit dice, and they can go "OH GOD RUN."

For my part, in my printout of the module, I crossed off that encounter and wrote this in instead: "Vargouilles in area 7 have supposedly made more vargouilles, so make this encounter just a vargouille spawn."