Latest blog post: An unforseen hiatus. (2023-01-02)
It would be risky to send out an invasion force with a crew who think they're on an exploratory mission; that could easily lead to mutiny from those who feel carrying out their orders to attack would make them the bad guys. I expect instead that your fleet is secretly looking for something or someone dangerous but not looking to be the one to start a fight.
It all started with an alien probe recording broadcasts from planet earth and bringing them to alien scientists. The alien scientists laughed and laughed at the amazing stupidity of the earthlings, and craved more. For budgetary reasons they could not get a probe for "entertainment", so instead made up a crazy "top secret" story about possible advanced ancient technology based on bad translations of b-grade movie "plan 9 from outer space" in order to get another probe sent towards earth.
Spies for other alien races noticed the secrecy and the probes and started sending own probes, which in turn got interest of yet other alien races as to why so many other alien races were sending probes towards earth, and it snowballed till everyone wants to know why everyone else is interested in earth, and rumours of an ancient weapon called "the solenite bomb" that can turn stars into exotic dark matter.
So now different alien groups are sending exploration fleets towards earth, with armed escorts to help deal with potential conflict with other aliens exploration fleets. This was the first fleet to arrive in our solar system.
You can't prove that this story isn't true!
That actually parses. Much like the theory snuck into very good book about first contact. That our first contact is millions of probes that have crashed into the earth for millions of years. We finally figure out what they are and...it's a damn chain letter with better graphics. Aww, well at least it wasn't an extended warranty on our planet.
There's also the question and the concern of the added logistics required to keep those military vessels going. Their maintenance schedules are very different from the optimized minimization of civilian or explorer vessels, designed to operate fairly independently. If they're worried about encountering something else out there on their level that might be aggressive, okay, maybe. But, if they're doing fairly routine exploration work, the additional military force doesn't make so much sense to be directly attached.
Eh, that constraint varies depending on how good the Alliance's maintenance game is. If the fleet has workshop ships capable of building replacement parts, and its warships are solidly built with long-lifespan components, then they could afford to be generous with combat units. On the other hand, if their warships are bleeding-edge things with lots of complex high-strain components, then they could indeed put a heavy load on the logistics side.
Given that the Alliance has been at peace for centuries, I expect that they're closer to the former scenario than the latter. Though even so, every warship they include is money they're not spending on another science vessel, so they have to draw the line somewhere. And of course, on paper they all have the same mission and face the same hazards, so they should all have the same force mix unless somebody knows that this particular fleet is headed for trouble.
has [a] significantly higher amount
This is indeed weird. I can think of any number of reasons an exploration fleet might go somewhere tooled up for heavy combat, even when other such fleets aren't, but hardly any of them include a reason not to tell the fleet personnel about it up front. If the Alliance had any major adversaries, then the secrecy might make sense, but they don't.