Door harness won't sit flush anymore

[MankDeems]

1) I am not a Ford technician
2)I watched zero videos before taking my 2 year old truck apart.
3) no it's not covered under warranty.

Okay with that out of the way why won't this stupid door connector sit flush anymore I didn't dicker the passenger when I did that side

Am I just anal OCD or is this not supposed to sit like hella flush and just clip in? I feel like it's important to not get water in my door harness connectors

*Took doors off to tap speaker wires for subwoofer amp's LOC, inside the pillar was the location I decided was sneakiest*

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[BlueSpec1]

The flexible duct's seal isn't seated onto the plastic base/grommet lip. I removed the base to seat them back on my Escape.

Another vehicle, same type of seal that fits over the grommet base's lip, then snaps into metal hole so the lip of the EPDM seals against the metal.

 

[Montana]

Looks like it might have just come loose? Is the plastic ring inside installed the correct way? It's not upside down or anything and just a one direction ring (can't say I've ever seen one any other way)?

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