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We also have this water collection occurring. I carefully wash it out with a spray nozzle when washing my X and then dry it with a rag. Ours tends to collect leaf debris in there as well so I'm fairly careful to get that out.
I use a pressure washer to rinse off the X when washing it. I make sure to spray near the drain holes every time but I wouldn't be surprised if they clog easily.
Thanks guys ... this is a nuisance .....totally a bad design. I wish like M3 owners there is an option to run a rubber tube around used for road noise reduction to fill that gap.