I jump-started my pc after installing my 3090 and I noticed that 2 out of the 3 fans were spinning. I was wondering if I should try to get everything set up then manually oc the fans or if I should start the return process.

I have the FTW3 Ultra 3090. I haven't even loaded windows onto the pc yet so I don't know the exact temps or etc. I also checked for any dents or any abnormalities in the fans and I didn't see anything.

Lucky you with that FTW3 Ultra 3090! Your card has EVGA 3rd gen smart cooling "ICX3"--it has 9 different thermal sensors and can run the fans asynchronously when it wants/needs to depending on hotspots on card.  So for example in your case, since you don't have OS installed yet and you were sitting there in BIOS marveling at all this cool hardware you just finished assembling ( I always do that too when the build's done ), probably the 2 fans over the GPU/VRM area spun up after a moment but the one over Mem didn't need to since you were displaying a simple image with almost zero changes ( Date & Time and maybe cpu & mem bus and clocks depending on which Mobo/BIOS ? ).  I understand why you'd think that fan spinning wasn't a good sign if you didn't already know all the above ( There's a cool brief informatic about 80% of the way down the overview tab for that card on EVGA's website that details it BTW ), but sounds like you have no worries yet. Now stop reading this and get Windows installed already so you can get to gaming!