Beer sour at bottling

We have started brewing all-grain. Our first batch was a 5 gallon mocha stout as follows:

Grain:
4.4 2-row pale
21 oz crystal (120 lovi)
10 oz Chocolate
10 oz Roasted Barley
17 oz Flaked Oats

Hops:
0.8 oz goldings (5%) for 60 min
0.5 oz goldings for 15 min

Misc.:
1/4 lb cracked coffee (steeped for 20 min at flameout)
4 oz Bakers unsweetened chocolate (in boil during last 5 min)
irish moss (last 10 of boil)
Danstar Nottingham yeast

We brewed using a 1 step infusion mash in a converted picnic cooler with copper tubing. Infusing the grain at 154 F for an hour, and sparging at 170. Our OG came to 1.4, and our final at 1.001. We left it in primary for 2 weeks, and left it for 6 weeks in the secondary. Everything looked as planned; the colour was great, the smell was great.

When we tryed the flat beer, it tasted sour. And not a good sour. We bottled it anyways with 3.8 oz of priming sugar, and let it carbonate. We tryed it yesterday (after 2 weeks in the bottles) and it was flat, no head, and was a gross kind of sour. we don't know what went wrong.

We are bottling a amber ale today and the flat beer tastes a bit sour, not as bad, but still undesirable (we'll see how it is after carbonating).
Does anyone know why this happened or how to prevent it?

Thanks

I wouldn't worry about it until it is carbonated and conditions for 3-4 weeks. Even then, if the sour is trending towards mellowing out, then just give it more time and it will eventually be gone.

Wouldn't hurt to give all of your equipment a good OxyClean soak before the next batch, though.

The stout has been in the bottles for almost 4 weeks now. I almost don't see it mellowing out, I'll definitely keep some for a few months to try later.

Are you fermenting in glass or plastic?

What is your cleaning/sanitizing regimine?

For the stout primary was plastic and secondary was glass.
For the red ale, both were in glass.

I wash the fermentors with diversol in hot water, rinse well, sanitize with iodophor.
I put a sanitized bung and airlock on the top until it's time to transfer the wort or beer into them.

Six weeks in secondary seems pretty long, and as far as I know, for such a small beer, pretty unnecessary. Then again maybe I'm wrong, but I usually bottle after just 2 weeks and let the brew condition while in the bottle. Was secondary a glass carboy? How much headspace was there? Did the airlock ever go without fluid, which would have exposed the brew to air?

Undesirable sourness is a decent indication of infection, and as many sources will tell you, if you're using plastic, it's hard (nearly impossible) to avoid further infection with future batches in the same plastic equipment, without very strenuous sanitizing procedures.

EDIT: Sorry, asked some of the same questions as above. Disregard anything already answered.

What I did for for a plastic bucket that produced vinegar beer: heat some water to about 150F and transfer to the bucket, dumping in a half cup of bleach as you go. Let it soak till it cools and replace the gasket in your lid. Also the transfer tubing is another possible issue. I prefer silicone because you can put that stuff in water that's 212F. Vinyl should probably have a replacement frequency but I'm sure you can sanitize that too.

Was it an infection?

I'm dealing with a very similar issue right now. In fact, it developed about the same way yours did and remained after carbonating for two weeks. I just tasted it after a month and the sourness seems to be mellowing a bit but the overall taste is still bad, maybe morphing into some other bad flavor. I plan to let it sit for several months and then make a verdict. It's my second brew so sad to have to dump 50 bottles down the drain. And believe me, if it still tastes like the the FBDU doesn't want it. Good news is, next two brews done in the same equipment seem fine.

More than likely an infection.

I had exactly the same issue with a Belgian Wit, all was fine till I bottled, then SOUR SOUR SOUR.

I took it to some experts, and was told it was an Aceto infection. I opened another bottle last week (I bottled this in Feb), and its still helluva sour, but there is still malt and I basically ended up with a Sour Berliner Weisse.

You got an infection, either Aceto or Lacto, its just a random bug got in yer beer (probably when you racked to secondary)....live and learn.

When I brewed my first AG, it was sour. It was my first ever that I had to pour out, and because I hate to lose, I waited almost a year before giving up. Since it was my first AG, I was expecting to have some sort of problems with efficiency or simply being unprepared. I was extra careful with cleaning/sanitizing because if it failed, I didn't want it to be something that I was experienced at such as cleaning, hitting temps, etc. (I am experienced at extract and partial mash brewing.)

With the help of people here, I finally realized what I did differently on this beer: I used tap water. I usually use bottled water and make dark or heavier beers. This beer was very light for my BMC friends, and did not have enough body/flavor to hide the chemicals in my city tap water.

Had my BMC friends been here and tried the samples, they would never try another homebrew. If it had been my first attempt at making my own beer, I would have quit that day because it would have killed my confidence. But, I have had success, so I knew it was something about my process that was different on that day. It took awhile to figure it out, but we did, and I have successfully brewed three more batches since. I am working on an AG today, the first one since that try, so it is on my mind again. But, I have my bottled water and it is a dark beer, so should be a win win this time.

So, go grab a beer, evaluate what you did and consider every step and ingredient. Then, you go try it again. Check this one again later, but don't give it a year like I did!