I just purchased a Fender Blacktop Stratocaster about three months ago (as of june 30th) and I am already noticing some rust/discoloration on the pickups and frets. Does anyone know if there is anything that I can do to stop this?

Where are you storing it while not being played?
Where do you live?
Is it humid where you live?
I would take it back and exchange it if only 3 months old.....should not be showing signs of rust at that young tender age

_________________
1986 Fender Sidekick Reverb 35
1990 Fender Red Knob - "The Twin"
1992 Fender Newporter - Acoustic
2000 Fender American Series Strat - Natural ash
2010 Fender Mustang 1
2011 Fender Blacktop Jazzmaster -Sunburst
2012 Fender Champion

The frets can't rust as they are not steel, give them a polish.
The pickup magnets are Alnico, and have no protective finish. They can rust. Give them a rub too.

Frets can rust- I had a bass that wasn't well taken care of and it had regular rust and greenish oxidation on the frets. It all cleaned up though and the shine came back.

Only steel rusts.
You are correct in using the term oxidation for the frets.
The OPs guitar is perfectly normal, and just requires the necessary maintenence.

When not in use I leave it on a stand, in an open room. Although it is normally humid where I live, it has been pretty dry for the past two or so months. I have tried polishing the frets, but that doesn't cut it, they are still discolored, sort of green in spots, and orange in others.

The frets are made from nickel silver, which mainly contains brass.
The sweat/salt from your fingers in the most likely cause for the corrosion, brass going green.
It could be that the frets are of a lower grade of material with less nickel.
Nickel silver is corrosion resistant, but not corrosion proof, I'm afraid.

Here's a pic:

Mask off your fretboard and polish the frets with a cleaner such as Brasso etc. I suggest that you not use steel wool as the fine particles can wreak havoc on your pickups and pots.I use an abrasive non-metalic pad such as Scotchbrite.A light rub with the pad on your pups should do the trick too.

_________________
'65 Strat,65 Mustang,65 Jaguar,4 more Strats,3 vintage Vox guitars,5 Vox amps,'69 Bassman with a '68 2-15 Bassman cab,36 guitars total-15asst'd amps total,2 vintage '60s Hammond organs & a myriad of effects-with a few rare vintage ones.

Well that does look like rust. It's orange/brown just like you might find on a frieght-train. Okay. There are some people with real acid type hands. I had a friend that could turn strings black in a matter of just a few days.

Yup I'm one of those guys... its funny its almost like something clinically wrong with me- my strings go out super quickly, and not only that but after a while I bleach shirts and stuff because of my sweat and oil (my mom hates it ) ... I'm slightly acidic I guess

its weird, but true

_________________
Kid: "Hey Smokey! Where did you get your name?"
Smokey the Bear: "Well..."
(former user jimbo612)

It could be from the strings, what are they like?

Those frets have already been cleaned there is sort of a tell tale white sticker or polish residue next to the fret.

Question is what were they cleaned with and was it polished off properly?

I tape off and use Brasso on my guitars especially on second hand ones.
It is time consuming but gets a mirror finish. I use paper towels to buff and remove the polish residue off completely.

Actually looking closely I should have buffed them before I took this shot.
This fingerboard was disgusting before I cleaned it.

This is a very, very common occurrence; it's simply one's body chemistry. I know a guy who by just 'reasonable' playing destroys a new string set in just one day. After a few weeks, his frets and fingerboard need a serious cleaning in spite of the fact that he stores the guitar correctly and fastidiously wipes the neck and board down after each time he plays. Even the coated sets last him only a few days.

_________________
You dig?

I am hard on strings, and I have heard of acitic hands, which is why I wipe off the strings everytime I'm done playing. But the strings that I just took off of it weren't corroded at all, they were just old so I decided to change them. Actually if you look closely, you can see "shiny" rust free spots where the strings were. Anyway, my problem with it is that it's brand new, frets shouldn't be able to actually "rust", and it's been well taken care of. When I clean it I usually avoid putting anything on it, I usually just wipe the body clean with a micro-fibre cloth, and sometimes (as in this case) scrub the frets with a scothbrite pad. As for the pickups, which I haven't talked about much, they have covers on them which are supposedly stainless steel, and they have a sort of rainbow effect on them. This may be removable, as I wasn't to worried about them until I noticed the frets. I'll try to post a pic of them shortly. On Monday I'm going to attempt to return the guitar, as I am sure that the frets themselves are rusted, not stained by something else, such as strings.