As usual, I used pliar to take out my center trace from my shutter.
But this time, it was stuck in their harder, so I used a little more force and it finally came out.
When I spun it on a pencil, it sounded different that before which really scared me,
Is it possible that I “crushed the bearing”?
“as usual” should never precede “I used a plier”. That phrase is best preceded by “as a final resort…”
If you don’t have a specialized tool for removing bearings, a 1/4" drill bit works dandy. This will save you having to use pliers.
I couldn’t say if you’ve crushed the bearing, mind you. What happens when you roll it along a flat surface? Does it still appear to be “true”? Not that the eye is the ultimate test, but if it seems out of round you don’t need to look any further. 
Something could’ve got into the bearing? Did u leave marks on the bearing?
You could also check the performance on another yoyo.
I’d really love to know what in the world people are doing that requires them to take the bearing out of their yoyo frequently or use pliers to remove a bearing ever.
OP, yes, you probably crushed your bearing by not being careful with the pliers, likely by pulling instead of wiggling. This is one of the risks of using the wrong tool for the job. Putting the bearing into a yoyo and throwing it would be an extremely easy way to find out if the bearing is destroyed or not.