As the title says believe one bolt hole is misaligned.
A little background:
My first Oil Change was a freebee from the Dealer. The 2nd was from a trusted mechanic. When I was at the Trusted Mechanic I was horrified at what I was witnessing when I peaked through the window. I don't need to elaborate, but to say, I understand torque, thread form, manufacturing and assembly issues. My former life.

Not wanting to be tortured again I decided I'd go back to changing my oil. How hard can that be?

So on my first change I find one of the skid plate bolts is missing. GREAT!! While under there I take one of the Skid Bolts and tried to thread it into that spot. It didn't go!!! This it the Front Drivers side BTW. Another great discovery, but of course there's a fix. I purchased a cheap set of chasing taps and dies from Harbor Freight.

Well it time for an oil change. I'm going to chase that while the oil is dropping. Just to make sure I have the right info on the tap size I compare my tap with one of the bolts. OMG, I think a Shop Class Student ground the tap! By Hand.

Good thing is I bought some 8.8 grade screws (don't know the OEM grade). I'm thinking this should be good enough to chase this hole. To my surprise, the bolt simply went in. No problem.

So now I'm finishing up the job and the bolt doesn't go?? I do everything I can think of. Loosen all bolts to move the plate.

Visually it looked good, but was a no go.

Since this is only my 2nd change I'm not so familiar with where things are. Is there by chance some threaded holes in the neighborhood needed for something I don't have?

In other words could I have checked the wrong tapped hole. BTW I noticed this one had a nice clear/clean grease drip exiting.

The holes for the skid plate are notorious for getting fouled up when a mechanic doesn't start the bolt by hand, especially the TRD Pro skid plate. It could also be that your skid plate is bent or warped which would put a hole out of alignment. The chassis holes are pretty accurate on location, but the holes do get dirty and need to be cleaned.

Many people replace the bolts with studs and nuts/washers; so much easier to line up the skip plate when installing it. There is a thread here that talks about it.

TRD Skid Plate Mounted w/ Studs 2010-2021

My Skid Plate is only 8months old and hasn't been bumped by anything.
Like I said, I'm not completely familiar with everything under the truck, but the hole I believe is for the Skid is in pristine shape. I easily threaded by hand a bolt till it bottomed out. The question still remains, did I pick the wrong hole? Guess I'll figure that out the next oil change.

Wish I had crawled underneath to look around before the first oil change, and inspected afterwords. Then I'd know who left that one out or if it was ever installed at the factory.

There are no other stray holes for mounting the skid plate. It’s possible that you got the initial bolt angle wrong and cross threaded it, which is why people are asking if the skid plate was bent resulting in misalignment of the holes. Your best option is to get under there with a flashlight to align the plate and insert the bolts by hand, as opposed to doing it by feel.

Given that this is just your second oil change on the vehicle, i can see a life of pain from installing this skid plate and would highly recommend doing the Saker Atud Mount conversion which I linked here.

Ok so you made me do it. Took it off to take another look.

There is another tapped hole and indeed the correct hole has been cross threaded.

Mystery solved.

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Well relatively speaking, for the job of reinstalling the front skid plate, that hole is not even on the fairway. IRRC, the OEM stamped steel skid plate has posts which poke into the larger circle(s), to the left of your red circle, which have the intended bolt holes in them. The TRD plates have spacers that neatly fit into those circles.

A couple of things to note...

If you notice on the skid plate, the front driver side hole is a regular circular hole but the other 3 are slots. When installing the skid plate you need to start with that hole first. Get a bolt started in that hole then the other holes have wiggle room since they are slots. If you don't start that hole first you may have a tougher time getting it to line up.

The skid plate is bolted to 2 supports that are replaceable as they themselves are just bolted on. So if any of the threaded holes get stripped or otherwise screwed up and you want to keep everything stock then you can just replace one or both of the supports as needed. In the picture posted in one of the above posts the silver colored bolt is threaded into one of the supports. You can see the head of the bolt that is attaching the support to the frame.

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Inserted photos for references.

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Went to the local Cutting Tool Distributor and bought a tap. Chased it and torqued the bolt. All good for now

Thank you!!

Thank You!!