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Sounds like the case itself may be warped.
It's going to be hard to fix. You may be able to sand down the area around the fan. Be sure to use fine grit paper, go slowly, and clean off any loose plastic bits afterward.
I'm guessing you already verified that everything's aligned properly and attached snugly.
Alternatively put a small insulator on top of the fan case so it keeps the laptop case away from the fan itself.
It may have come with this and it broke down over time.
I've used Goop adhesive like this on a very old ~~Dell~~ Lenovo X series. Ran a bead on top of the main fan body because it would vibrate against the plastic part of the case, but only when my wrist was on the keyboard.
Nice thing about Goop is it remains rubbery, and you can smooth it down while it's still wet to make it as thin as needed (just lick your finger and it won't stick to you).
Goop is freakin' magic glue. I've glued laptops back together with it, yet it's removeable too.
That's a good suggestion, I'll try some kind of temporary bits of padding first to try and work out what is going on. It is a plausible explanation of how the problem appeared, because I can't see anything wrong
Actually, yes, listen to this guy. Try what he says before you do what I said.
Additive repairs are safer than destructive repairs.
The problem with finding where and how to make adjustments is I can't work out the physics/engineering of what is causing it, or what the original design was meant to be like. But the other comment does sound useful in this way
If the computer is flipped upright but the bottom is off does the fan rub?
I haven't tried that, sounds like it's worth a check