Has the car been recently assembled? Other than a too thick seal, it could be a few other things. First, if you are only getting one click with the latch, you're on the safety/secondary, move the striker outward until you get two clicks. Also, check to see if the vent window frame is binding at the pillar seal. Another possibility is front of door is adjusted in too close to hinge pillar, causing a pinch in seal.
Last resort, adjust striker to get door in the hole and leave it shut for a couple of weeks.
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