You are paying for a service to be performed. They are not doing this for free as a favor to you. You have every right to expect it to be don't right. If not you should say so. You don't have to throw a fit and be an A-hole about it, but you have the right, no, the responsibility to let them know what they are doing is wrong.
In my opinion arrows are the MOST important piece of a equipment in the equation of accurate archery. And they are not cheap, even moderately priced ones are still fairly expensive per dozen compared to other items. I would not accept poorly fletched ones. And if your arrows are as bad as you make them sound, they are not poorly fletched, they are horrible. With most of the fletching set ups I have seen in shops you would have to do that kind of work on purpose, not by accident.?[

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I don't know if there is much you can do if you already paid for them and took them home, but you could try. If you wanted to you could go back to the shop and talk to the owner/manager and see who fletches their arrows for them. Then politely tell them the problems you have and show them some if they care to look at them. If they don't offer to fix them or something then this would be a good time for you to learn to fletch your own arrows

. Some people enjoy it, I personally hate it. Least favorite thing about archery to me. If I were not dirt poor I would get knew arrows when they needed re-fletched to be honest.
Or I would look for a new place to buy my arrows from, probably not a bad idea any way to be honest. You don't have to buy all your crap from one place. Nothing wrong with spreading the wealth around. I buy my bows from one of two places, but most of my small stuff at other places, even cabelas sometimes if they have what I want (I live near one, I don't order anything unless I have to).
I get my arrows from a place pretty close to me. Now that I moved it is actually only about a block or so away. I'm not real picky about what my arrows look like, so I can usually go in and pick some aluminums already fletched with feathers. I don't care what colors they are so I don't usually have any trouble getting them on the spot. And he will cut them and glue in inserts or points while I watch. It only takes him a few minutes.
If I want Nitro Stingers I have to order them though, he doesn't carry them in stock. And if I want target type stuff there is a shop about half an hour away in Ohio that I go to.
I have to be honest, I have never seen or heard of arrows messed up to the degree you are talking about come from any shop near me, and I have quite a few in my area. If I ordered arrows and they looked like that I would throw the Bull S*&t flat right on the spot and want to know what they were smoking when the fletched them. And if they shared I might consider coming back

. ( Just joking, I don't do that kind of stuff anymore)
So the short answer is "No it is not bad etiquette to complain about bad service when you paid for it.".
Good luck and let us know how it comes out. If they don't fix the problem let us know the name of the shop and where it is so others can avoid it, or at least not get arrows there.
Paul