Why do some balloons have those dark dots at the top even when blown up?

First you need to understand how balloons are made.  A balloon-like shaped mold is dipped into a vat of coloured latex, and the mold is coated.  Think of dipping a frozen ice cream cone in chocolate.  When you pull the ice cream out, a thin layer of chocolate the same shape as the ice cream forms around it.  This is how balloons are made. 

Now the dots are more apparent on cheaper balloons.  Why is that?  It has to do with how the balloons are dried.  Think again back to the ice cream example.  If they are dried upside down, just like holding the ice cream upside down while the chocolate sets, more chocolate will pool at the tip.  In the same way, more latex will pool at the base if the newly formed latex balloon is drying upside down.

If it is dipped and then flipped so that it dries right-side up, then less latex pools at the top, and the dark spots are less apparent.  The reason why some manufacturers dry upside down is because it is cheaper.  Drying right-side up is more expensive, and so generally is done by balloon manufacturers producing higher quality balloons. 

However, keep in mind the more inflated the balloon, the less apparent the dot.  If you purposefully underinflate the balloon for balloon sculpture purposes, be aware the dot may be more visible.