l own a 07 scion Tc. l havent taken it to the dealer for any of these problems yet.
l got the blue Light kit for under the dash from the dealer and its only attached by zip-ties and hangs down to where you can see the bulb.
i also got the bazooka subwoofer. (i know it sucks) but the box doesnt fit like it should against the side of the trunk. theres a space of like 2 in. that l can move it.
Theres a spot on the drivers seat that l have no clue how it got there. l never spilled anything on it except rain water. ive tried to clean it and it wont go away.
Also has anyone Noticed the paint scratches if you look at it wrong?
If anyone can give me some info on any of these problems l would greatly appreciate it.

l also got the 07 tC about 2 months ago. My blue led lights r attached in the same fashion & for the price l was not impressed. l can not complain though because at least there r no unsightly wires. It is also good to have the button that turns them on & off integrated into the dash. Aftermarket kits r annoying because the controls to turn them on an off r not as neat. So l think it is good that we opted for these & not others.
l dunno about the Subwoofer. l almost got it but then realized it would be dumb since l usually listen to country. :-D Plus l like being able to lay in the back with the seats down at the drive-in. Maybe u could bring it to the dealer & ask them why it does not fit flush..
As far as scratches go mine is Nautical blue & l have noticed that if u look at it at a certain angle it looks like there r tons of tiny scratches. Are all cars like that? l will have to further investigate. On the other hand it does scratch very easily. My first one came from my xm radio antenna.
Did u get rear tail lights by TYC? l noticed that the corners of the molding r scratched where they installed the tail lights & one side of the body does not look flush with the car.

My seats have been fine other then little nags when my ring gets caught or something.

1) The light kit, u might want to ask the service department how they would install the kit normally. Since ALL accessories r put on the car after u order it. Since u can see the bulb it might be too low. l would ask to have it installed properly.

2) l do believe the bazooka subwoofer was originally designed for the trunk spaces of the xA & Xb, so it might have more of a difficult time properly fitting in the trunk. It supposed to be tied/screwed down.

3) l have a spot on my seat as well, not sure how it got there. Did u have fabric guard applied to the seat? That is the only thing l could think of it that might have caused a stain.

4) All cars have scratches in the paint, just depending on the angle u look at the car. No car is ''flawless'' off the lot. To determine if the scratch is really deep, just run ur fingernail over it gently, & if u can feel a dip, then its a scratch.

Seems like u have most of ur questions answered, the only thing l can think to add is this: My buddy has an 06 Tacoma & even if u spill water on his seats, they stain. l have no clue as to why. But l think Toyota seats in general just do that. l know it hurts to have a stain in ur beautiful new car but sometimes it is best just to let it go. Some stain removers can make it worse. Seats will eventually get stained ur best bet is to just keep trying to prevent new ones. =( The scratches car normal, they can even be caused by dust blowing but the guy above me is right, the whole fingernail trick. You can try buffing them & see if that helps any. The lights & sub r just bad because they're dealer installed. You would been better of buying the lights & sub separate & having them installed by people who know what their doing. You can try to mount the lights better with screws but that might void some warranty. Would not hurt to take it back & have them look at it. Good luck.

l can not help u with the subwoofer or the lighting kit because, l dont have them & l know nothing about them. What l do know is that ANY water u get on the seats makes like a white stain on that area. l know but l talked to Toyota/Scion & they said that they know about the problem & they r looking to go to a seat in 09 that doesnt do that. But there really is nothing that u can do.
l have 2 BIG spot on my passager seat because my GF just got out of the shower & her hair was still wet..

Yes! Despite people making the claim that all car paint scratches & chips (which is true), I've noticed that my 2007 Azure Pearl Scion tC scratches & chips very easily. Other problems that I've experienced r annoying rattles, the fake aluminum also easily scratches, & the car sounds retarded at idle (supposedly due to the fuel injectors). These cars r priced so low because of all the short cuts that were taken. l would say its worth it, but the tC is not a refined vehicle by my reasonable standards.