To be measurable is a relative notion : you are measurable for a specific $\sigma$-algebra. You seem to be confused and to think that being measurable is an internal property...measurability is defined after having defined a $\sigma$-algebra
So, if you have a $\sigma$-algebra $\mathcal{B_1}$, you can take a collection of non-measurable set (for $\mathcal{B_1}$) and consider the $\sigma$-algebra $\mathcal{B_2}$ generated by this collection. Then your sets will be measurable for the new $\sigma$-algebra $\mathcal{B_2}$ BY DEFINITION of measurability. This is just that $\mathcal{B_2}$ has no reason to be included in $\mathcal{B_1}$
On the other hand, if you take a collection of measurable (still for $\mathcal{B_1}$) sets as a generator, then you will indeed create a sub $\sigma$-algebra of $\mathcal{B_1}$. But this is not the case in general