My tyre usually got a lot of small tiny bits of stones stuck inside the tyre tread. Every time I painstakingly remove them, then after one week or so, got lots of small stones again.

Do they harm the tyre badly if I just leave them??

It's normal, don't worry. Its a good indicator of your treads. Bigger stones = deeper treads

good way to look at the issue

lols, its like you made a cut to your hand and its bleeding, and you said, oh hey, i'm alive! cause i'm bleeding!

nope, its a different analogy.

a more appropriate one is that you got cut on your hand and you looked at the fast or slow bleeding to determine if you have high or low blood pressure