Motherboard not sitting write, standoffs too short

I remember having this sort of problem. Not really assad as yours, I could fit everything and attach everything what seemed properly just when I would put the hdmi or dpcable into the gpu the bottom row of ports would he a little restricted. I had and 011 air I cannot be 100% it was this case though, I just remember that's ehay problem I had sometime in the past.
 
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