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I was on the track yesterday, all was fine for about the first hour or so and then I noticed that my bike was really hard to shift into 3rd gear. It would go from first to second easy as usual and then when I tried going into third, it just wouldn’t shift until about my 5th or 6th attempt but I was slowing right down. I kept trying and trying and I ended up going off of a jump and when I came back down I felt something In the bottom up kinda make a clunk feel and then it would shift normally. Shortly after it had issues shifting into third again. Not sure what would cause this but maybe somebody has got some ideas??

What model and year is the bike?
Has it ended up on the shifter side recently and hit the shift lever?

It is a 2005 Honda crf450r. And no it hasn’t. I verified that the shifter isn’t hitting the case either

I have seen a bent shift fork cause what you are describing.

2nd the bent shift fork.

So how should I go about checking that? I’m
Not too experienced on the bottom end of the motor? And I didn’t crash it or anything so is there any reason why it would bend?

It happens from hard force against the shift drum and usually results in opening / bending the shift fork. Can be a over excessive force while pumping on the shift lever up or down, from a crash which transmits force to the fork & drum. It could be from landing from a jump with your foot on the lever transmitting undue forces on the shift fork & drum. It could just be wear from use.
If you have never had a lower end apart it's going to be a intimidating job. Much depends on your mechanical skill level.
I would do some more investigation before jumping to any conclusion. With the bike on a stand statically going through the gears as you rotate the rear wheel. I would also try in on the stand with the bike running and see what you find.
It is certainly something that need to be investigated fully before going in.