I bought a trek Fx 7.1 back in October since then I've had to have the wheel "rebuilt" because the ppl at the bike shop said the spokes were "like spagetti strings", went to get a tune up and they told me that spoke was broken and yesterday I had a flat and they told me that another spoke was broken. Please bear in mind that I wasn't riding in the winter. I live in NYC and some of the roads are crappy but for the most part I try and avoid pot holes and usually only carry gym stuff on the rack. Could this just be a bad wheel or am I doing something wrong?

It sounds like whomever rebuilt your wheel did not do it properly.

Flats and broken spokes are separate entities. Most spoke failures are due to insufficient tension from the initial build - which they should have checked and adjusted when you first had to have a spoke replaced.

If their "rebuild" included a relace with new spokes, then you really shouldn't be seeing these issues unless the wheel is totally unsuited for your weight/strength. If their rebuild only featured tinkering around with your existing spokes you shouldn't really be seeing these issues either, unless you bought a used bike or have managed to log some serious mileage since purchase. But if it is a used wheel, and it's begun to pop spokes - then it can certainly be prone to keep popping spokes until you either get a new wheel or have it rebuilt with new spokes.

Bad batches of spokes have happened, but they usually make themselves known through the community.

On average I ride about 12 miles a day once in a while I'll go on longer ride...Would you guys suggest just repairing the current wheel and replacing spokes or gettting replacing the wheel all together?

If it was bought new in Oct, you should have taken it back to the Trek dealer, and they should have sorted this under warranty; spoke breaking isn't somthing which happens with normal use in 6-8 months, it was most likely either faulty components or badly built to have that short a life.

If 2nd hand, would find another LBS who know how to build wheels.

That really depend on how you value your time, and the consequences of getting stranded. A poorly built wheel that's been ridden some is likely to have had the spokes weakened all over, so it may well continue to pop a spoke every now and then - even if you have them brought up to proper tension. If you can live with this (particularly for 36/32H wheels losing one spoke is pretty much a non-issue, they remain straight and rideable anyhow) then there's no need to do anything apart from replacing as needed.
But it can sure be a PITA to have such a string of nuisance failures, so a full rebuild with new spokes can be both cheaper and a lot less hassle. If bought new in oct you should have plenty of life left in the rim.

OTOH wheels, as bikes, are usually cheaper bought whole than in parts, so it might make financial sense to go for a brand new wheel instead.
Set aside some mone to have it checked over before you start riding though.

I have this aversion of buying more than needed, even if it makes financial sense, so I would probably go for a rebuild.

So you've had your wheel rebuilt by the LBS at their recommendation and now the re-built wheel is breaking spokes. I have a few questions though, how much do you weight and are you hitting potholes while riding?

I would certainly bring it back to the LBS for a chance to make amends since they re-built the wheel, but bear in mind that once spokes start to break they continue to. Do you know the condition of the existing rim before they re-built the wheel? I'm wondering since you've already sustained broken spokes with this rim before the re-build.

I weigh about 195-200lbs and I usually have a pair of sneakers and a gym clothes on my rear rack (another 5-6lbs if that)...I ride in NYC so there are some crummy roads but I try my best to avoid potholes but there is a road that is just not well paved that I ride on regularly....On bumps I usually stand to avoid putting extra pressure on the back wheel...

I don't know the condition of the wheel...it's my first real bike..I belive I got it in early October and before the end of the year the bike was brought in and the wheel was rebuilt. So, I can't imagine that the wheel would be in horrible/bad codition...

Trek should warantee the wheel.
I am a broken record on this, but you should be on a 36 double butted spoked wheel.

The wheel has already been re-built by the LBS, TREK will tell him that their obligation is done. He needs to go back to the LBS. 32 spokes should be fine for his weight, 36 would be better, but 32 spoke wheel should not be breaking spokes unless the LBS is re-using a out of round wheel and varying tension to get a true wheel.

OP, is there any way for you to check tension on the spokes? Sometimes you can tell there is tension difference by squeezing them together even if you can't tell how much tension there is.