I noticed that my passenger door was making a squeaking noise just as it closed to latch. Upon some inspection, it appears that the plastic seal at the bottom of the door is rubbing on the frame. From the looks of things, it is now causing some surface rust and you can see where it ripped the rubber seal on the body. I'm going to get the paint fixed so that it doesn't spread, but I think that the door needs to be adjusted.

If it doesn't need adjusting, the plastic runner may be warped. I don't know if it is supposed to look this way or not.

 

Chicken or the egg? Yours looks like it got trapped/pinched...those cut marks are highly symmetrical. We got a door that has that vertical crease (stress crease) in outer door skin from the door being blown open forcefully, and it likewise has a split inner door seal and appears to 'drag' just a bit at closure, but it does not have any 'cut' marks like yours; it's just detached from where the seal connects to it's base connection strip. Had several doors on ours that creaked a bit at the hinges; that just needs lubrication to resolve.

I just bought a replacement for my driver's side, inner door seal on ebay (from Latvia, IIRC)...a new part for about $108 all in/delivered. Audi dealer wanted $220 for same part #. I also saw some recyclers selling used door seals online, which I thought was novel...askng $70 for a door seal older than my own car, LOL! On mine, I don't think the seal failure is related to anything other than dragging feet on it a bit when getting into the car. The driver's door is the only one with any wear on it, which is what I would expect. I too wondered about the bottom seal on the door possibly scraping a bit, but my door seal is messed up right where you'd pull your leg over the threshold, whereas yours is very distinctly been punctured quite precisely on the outer edge of the inner seal, but does not appear as separating from the base; just punctured.

 

So you are thinking the seal had that happen and it is bad or the hinge is bad and blew out? I am kind of thinking that it is the hinge, I found some similar threads in the A4 forum but this is all just guessing.

 

Opinion: Those two marks on that inner door seal are so specific; see if they align with anything on the door that could possibly have resulted in said damage to the seal. From the pictures it appears that you have impact marks in the lower sill panel, etc., so maybe an impact occurred and has slightly changed the swing/alignment of the door. You can measure the seam gaps going around to see if anythings 'off' about it. That outer, lower-panel, inside-the-door fitting/seal may have come loose or gotten misaligned from the prior impact to that region, and is dragging that edge. I don't think the hinge itself is 'bad', but if you check/adjust everything else that could be cause of the paint drag on the sill, then it may require a small alignment adjustment. Do the easy stuff before messing around with the hinge, other than lubing it if needed.