The upside down wouldn't have done any harm. Sometimes a bit of air can get in the pipe, which makes the lever go spongy, but bike brake cyinders are self bleeding, so the air comes back out after you press the lever a few times. that's nothing to do with your problem though. It's probably just a bit of contamination that'll burn off on the first heavy use.
It's always worth re-aligning your calipers in case they did a bad job in the factory. You should do that on any new bike. Loosen off the two caliper screws until the caliper can move sideways in the slot, then hold on the brake, which will centralise and straighten the caliper. Tighten the two screws while you're holding the brake on.