Trauma from cheek biting can cause bleeding of the cheeks if you are biting them that hard.
When you originally asked the question, you never mentioned that as a habit. I read it as they appeared and you only noticed them by feeling them with your tongue, then when you looked in there you saw blisters that were filled with blood.
This is the reason I searched my resources over for blisters that appeared on their own. So, as I stated before, I found that recurring blood blisters in the mouth are secondary to something else going on.
Cheek biting doesn't usually appear as tiny little blood blisters, it usually is a larger traumatized area. This is the reason for me not saying it was cheek biting. Again, I am not trying to scare you, but telling you what I found.
If you are constantly chewing your cheeks then you may notice traumatized tissue on both sides and blood may be present. If you have already had blood test done recently and all was normal then you could be dealing with cheek biting.
Sorry did not mean to scare you.